[gmx-users] Capping residues

Discussion:

Sai Pooja

2010-06-30 21:53:58 UTC

Hi,

1) What capping residues are recognized by charmm implemented on gromacs in
the latest git version?
I was trying to use ACE for acetyl but it is not recognized by pdb2gmx.

2) Is it possible to define caps at residues other than those at the
termini?

Regards
Pooja

--
Quaerendo Invenietis-Seek and you shall discover.
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Justin A. Lemkul

2010-06-30 23:57:11 UTC

Permalink

Post by Sai Pooja
Hi,
1) What capping residues are recognized by charmm implemented on gromacs
in the latest git version?

It looks like there aren't any. Check the .rtp file to be sure.

Post by Sai Pooja
I was trying to use ACE for acetyl but it is not recognized by pdb2gmx.
2) Is it possible to define caps at residues other than those at the
termini?

What exactly do you consider a cap? Usually a capping residue is applied only
to N- and C-termini. If you're trying to make some sort of modified sidechain,
then you have to look into parameterizing it yourself.

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

Post by Sai Pooja
Regards
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.

Mark Abraham

2010-07-01 00:39:59 UTC

Permalink

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Thursday, July 1, 2010 9:58
Subject: Re: [gmx-users] Capping residues
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Post by Sai Pooja
Hi,
1) What capping residues are recognized by charmm implemented

on gromacs in the latest git version?
It looks like there aren't any. Check the .rtp file to be sure.

There aren't. I had a discussion with Par Bjelkmar a while back about including some, but I don't recall the outcome.

Mark

Post by Sai Pooja
I was trying to use ACE for acetyl but it is not recognized by

pdb2gmx.>

Post by Sai Pooja
2) Is it possible to define caps at residues other than those

at the termini?
What exactly do you consider a cap? Usually a capping
residue is applied only to N- and C-termini. If you're
trying to make some sort of modified sidechain, then you have to
look into parameterizing it yourself.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin

Post by Sai Pooja
Regards
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.

--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Sai Pooja

2010-07-01 19:46:11 UTC

Permalink

Would it be possible to add some capping residues (like --COCH3 and --NHCH3)
by writing a separate .itp file and including it in the topology file? Is
there a way to make it consistent with charmm forcefield?

Can this be done alternatively by modifying the .rtp file? If yes, what
other operations must one do before using these .rtp files?

Post by Mark Abraham
----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Thursday, July 1, 2010 9:58
Subject: Re: [gmx-users] Capping residues
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Post by Sai Pooja
Hi,
1) What capping residues are recognized by charmm implemented

on gromacs in the latest git version?
It looks like there aren't any. Check the .rtp file to be sure.

There aren't. I had a discussion with Par Bjelkmar a while back about
including some, but I don't recall the outcome.
Mark

Post by Sai Pooja
I was trying to use ACE for acetyl but it is not recognized by

pdb2gmx.>

Post by Sai Pooja
2) Is it possible to define caps at residues other than those

Post by Sai Pooja
Regards
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.

--
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Justin A. Lemkul

2010-07-01 20:58:42 UTC

Permalink

Post by Sai Pooja
Would it be possible to add some capping residues (like --COCH3 and
--NHCH3) by writing a separate .itp file and including it in the
topology file? Is there a way to make it consistent with charmm forcefield?

No, because you have to specify bonds between these capping residues and your
protein. If you're #including them as new [moleculetypes], then you can't add
these bonds.

Post by Sai Pooja
Can this be done alternatively by modifying the .rtp file? If yes, what
other operations must one do before using these .rtp files?

Sai Pooja

2010-07-01 21:27:06 UTC

Permalink

I am sorry if I did not frame the question correctly, but putting it very
simply, is there a way to use capping residues with the charmm forcefield if
the residues are --COCH3 and NHCH3?

Post by Justin A. Lemkul

Post by Sai Pooja
Would it be possible to add some capping residues (like --COCH3 and
--NHCH3) by writing a separate .itp file and including it in the topology
file? Is there a way to make it consistent with charmm forcefield?

No, because you have to specify bonds between these capping residues and
your protein. If you're #including them as new [moleculetypes], then you
can't add these bonds.
Can this be done alternatively by modifying the .rtp file? If yes, what

Post by Sai Pooja
other operations must one do before using these .rtp files?

Reading in the manual about the file format? I don't understand your
question entirely. All the other force fields use .rtp entries for caps, so
I don't see why this couldn't be done.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Mark Abraham

2010-07-02 03:39:34 UTC

Permalink

----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>

I am sorry if I did not frame the question correctly, but putting it very simply, is there a way to use capping residues with the charmm forcefield if the residues are --COCH3 and NHCH3?

Yes - you edit a copy of the .rtp file in your working directory and add whatever you want. Here's what I use in CHARMM

[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O

[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33

[ impropers ]
N -C CH3 HN
-C CH3 N -O

Mark

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Sai Pooja

2010-07-02 11:05:21 UTC

Permalink

Thanks Marks. I tried it but this is what I get:

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Do I need to edit the aminoacids.n.tdb file as well?

Pooja

Post by Mark Abraham
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu, Discussion list for GROMACS users <
gmx-users at gromacs.org>

Post by Sai Pooja
I am sorry if I did not frame the question correctly, but putting it

very simply, is there a way to use capping residues with the charmm
forcefield if the residues are --COCH3 and NHCH3?
Yes - you edit a copy of the .rtp file in your working directory and add
whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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Justin A. Lemkul

2010-07-02 14:50:00 UTC

Permalink

Post by Sai Pooja
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb file as well?

What are you choosing as your termini when running pdb2gmx? It should be
"none," since by capping, you are not choosing a protonation state for the N-
and C-termini.

-Justin

Post by Sai Pooja
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham <mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at gmail.com>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>

Post by Sai Pooja
I am sorry if I did not frame the question correctly, but putting

it very simply, is there a way to use capping residues with the
charmm forcefield if the residues are --COCH3 and NHCH3?
Yes - you edit a copy of the .rtp file in your working directory and
add whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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Sai Pooja

2010-07-02 21:43:16 UTC

Permalink

I used -ter option and selected "none" for both terminal ends but I still
get this error:

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.

In the pdb file, this is what the capping residues look like:

ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17 FR1

ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60 FR1

Post by Justin A. Lemkul

What are you choosing as your termini when running pdb2gmx? It should be
"none," since by capping, you are not choosing a protonation state for the
N- and C-termini.
-Justin

Post by Sai Pooja
Pooja
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at gmail.com>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>

Post by Sai Pooja
I am sorry if I did not frame the question correctly, but putting

--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Sai Pooja

2010-07-03 19:32:40 UTC

Permalink

Follow-up.
It is easy to make it work. Just needed to be more rigorous. Thank you.

Post by Sai Pooja
I used -ter option and selected "none" for both terminal ends but I still
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60 FR1

Post by Justin A. Lemkul

What are you choosing as your termini when running pdb2gmx? It should be
"none," since by capping, you are not choosing a protonation state for the
N- and C-termini.
-Justin

Post by Sai Pooja
I am sorry if I did not frame the question correctly, but putting

--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
Quaerendo Invenietis-Seek and you shall discover.

Justin A. Lemkul

2010-07-03 20:41:10 UTC

Permalink

Post by Sai Pooja
Follow-up.
It is easy to make it work. Just needed to be more rigorous. Thank you.

It would be helpful if you describe what you mean. This error message is new to
me, and appears to reflect new mechanics in the upcoming Gromacs release. If
you describe what the problem was, how you resolved it, what your pdb2gmx
command line was, and anything else that might be useful, that would likely help
others solve this issue in the future.

-Justin

Post by Sai Pooja
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <saipooja at gmail.com
I used -ter option and selected "none" for both terminal ends but I
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60
FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80
FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
FR1
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul <jalemkul at vt.edu
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb file as well?
What are you choosing as your termini when running pdb2gmx? It
should be "none," since by capping, you are not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>,
Discussion list for
GROMACS users <gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>>>

Post by Sai Pooja
I am sorry if I did not frame the question correctly,

but putting
it very simply, is there a way to use capping residues with the
charmm forcefield if the residues are --COCH3 and NHCH3?
Yes - you edit a copy of the .rtp file in your working
directory and
add whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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Can't post? Read
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--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Quaerendo Invenietis-Seek and you shall discover.
--
Quaerendo Invenietis-Seek and you shall discover.

Sai Pooja

2010-07-07 20:29:03 UTC

Permalink

I checked again and the error does not go. Please read the steps below.

The pdb file I started off with did not have any hydrogens. However, the way
I had specified the capping residues in the .rtp file (SEE MARK'S MAIL), I
had to specify hydrogens in the pdb file for the capping residues. So I used
pymol to add hydrogens to my pdb file. I then used this file with charmm
force field. However, pymol had added hydrogens everywhere and this was
different from the definition of the standard residues defined in the .rtp
file. I could not directly use -ignh because I needed the hydrogens for the
capping residues. So I created a file that contained the hydrogens on the
capping residues only. This resolved the error related to hydrogens.

Error-from previous mail-NOT RESOLVED
(Fatal error:
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
I have used Mark's definitions for capping residues in the rtp file.

In the pdb file, this is what the capping residues look like:

ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60
FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80
FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
FR1

ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1 )

The error stated in the previous mail(quoted above) occurred when I chose
"none" for the both terminals or the carboxylic terminal option (using
-ter). It worked fine if I chose "none" at the N terminal and any other
option except "none" at the carboxylic acid terminal.
So I chose "none" at N terminal and some option randomly at the carboxylic
acid terminal. As expected, it adds a terminal at that end of the residue
before my capping residue which is something I DONT want. I havent been able
to find a way around it. Interestingly, when I generate a pdb file using -q,
and open that pdb file in pymol, I dont get the terminal carboxylic acid
that pdb2gmx gives in the .gro file.

I am not sure how to correct this. One way would be to remove those entries
from the final .gro and .top file but not sure if that would be right.

Pooja

Post by Justin A. Lemkul

Follow-up. It is easy to make it work. Just needed to be more rigorous.
Thank you.

It would be helpful if you describe what you mean. This error message is
new to me, and appears to reflect new mechanics in the upcoming Gromacs
release. If you describe what the problem was, how you resolved it, what
your pdb2gmx command line was, and anything else that might be useful, that
would likely help others solve this issue in the future.
-Justin

I used -ter option and selected "none" for both terminal ends but I
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60
FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80
FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
FR1
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul <jalemkul at vt.edu
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb file as well?
What are you choosing as your termini when running pdb2gmx? It
should be "none," since by capping, you are not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>,
Discussion list for
GROMACS users <gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>>>

Post by Sai Pooja
I am sorry if I did not frame the question correctly,

but putting
it very simply, is there a way to use capping residues with the
charmm forcefield if the residues are --COCH3 and NHCH3?
Yes - you edit a copy of the .rtp file in your working
directory and
add whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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-- Quaerendo Invenietis-Seek and you shall
discover.
-- ========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Quaerendo Invenietis-Seek and you shall discover.
--
Quaerendo Invenietis-Seek and you shall discover.

--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Justin A. Lemkul

2010-07-07 20:47:33 UTC

Permalink

Post by Sai Pooja
I checked again and the error does not go. Please read the steps below.
The pdb file I started off with did not have any hydrogens. However, the
way I had specified the capping residues in the .rtp file (SEE MARK'S
MAIL), I had to specify hydrogens in the pdb file for the capping
residues. So I used pymol to add hydrogens to my pdb file. I then used
this file with charmm force field. However, pymol had added hydrogens
everywhere and this was different from the definition of the standard
residues defined in the .rtp file. I could not directly use -ignh
because I needed the hydrogens for the capping residues. So I created a
file that contained the hydrogens on the capping residues only. This
resolved the error related to hydrogens.

Probably an easier and more reliable approach would simply be to create an .hdb
entry for your capping groups.

Post by Sai Pooja
Error-from previous mail-NOT RESOLVED
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60
FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80
FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
FR1

Maybe this is just showing up incorrectly in my mail client, but I wonder if
that CH3 is somehow misaligned and therefore not correctly identified. I
presume that you changed the residue name in the .rtp file accordingly? I
suppose the error message would be different (something like "residue not
found") but I just want to make sure. Mark's entry used NAC.

Post by Sai Pooja
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1 )
The error stated in the previous mail(quoted above) occurred when I
chose "none" for the both terminals or the carboxylic terminal option
(using -ter). It worked fine if I chose "none" at the N terminal and any
other option except "none" at the carboxylic acid terminal.
So I chose "none" at N terminal and some option randomly at the
carboxylic acid terminal. As expected, it adds a terminal at that end of
the residue before my capping residue which is something I DONT want. I

So does pdb2gmx somehow add the C-terminal cap after the carboxylate terminus?

Post by Sai Pooja
havent been able to find a way around it. Interestingly, when I generate
a pdb file using -q, and open that pdb file in pymol, I dont get the
terminal carboxylic acid that pdb2gmx gives in the .gro file.

So the cap is applied properly in that structure?

Post by Sai Pooja
I am not sure how to correct this. One way would be to remove those
entries from the final .gro and .top file but not sure if that would be
right.

This all sounds very fishy. This may be worth a bugzilla entry, but only if you
can build the structure in a very sound way, probably using .hdb entries (or an
appropriate all-atom structure, which you've yet to demonstrate).

-Justin

Post by Sai Pooja
Pooja
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul <jalemkul at vt.edu
Follow-up. It is easy to make it work. Just needed to be more
rigorous. Thank you.
It would be helpful if you describe what you mean. This error
message is new to me, and appears to reflect new mechanics in the
upcoming Gromacs release. If you describe what the problem was, how
you resolved it, what your pdb2gmx command line was, and anything
else that might be useful, that would likely help others solve this
issue in the future.
-Justin
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
I used -ter option and selected "none" for both terminal ends but I
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
I have used Mark's definitions for capping residues in the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00
1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00
0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00
2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00
1.60 FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
atom N not found in buiding block 1ACE while
combining tdb
and rtp
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb file as well?
What are you choosing as your termini when running pdb2gmx? It
should be "none," since by capping, you are not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au> <mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>,
Discussion list for
GROMACS users <gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
<mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
<mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>>>>

Post by Sai Pooja
I am sorry if I did not frame the question

correctly,
but putting
it very simply, is there a way to use capping residues
with the
charmm forcefield if the residues are --COCH3 and NHCH3?
Yes - you edit a copy of the .rtp file in your working
directory and
add whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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<mailto:gmx-users at gromacs.org>>
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<mailto:gmx-users at gromacs.org>>>
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Please search the archive at
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Please don't post (un)subscribe requests to the list. Use the
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<mailto:gmx-users-request at gromacs.org
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Can't post? Read
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-- Quaerendo Invenietis-Seek and you
shall discover.
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Please search the archive at http://www.gromacs.org/search
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Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- Quaerendo Invenietis-Seek and you shall discover.
--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Please search the archive at http://www.gromacs.org/search before posting!
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--
Quaerendo Invenietis-Seek and you shall discover.

Sai Pooja

2010-07-07 22:32:09 UTC

Permalink

This probably is my ignorance but the error and the "bug" goes when I
replaced CBX with NAC everywhere.

Post by Justin A. Lemkul

Post by Sai Pooja
I checked again and the error does not go. Please read the steps below.
The pdb file I started off with did not have any hydrogens. However, the
way I had specified the capping residues in the .rtp file (SEE MARK'S MAIL),
I had to specify hydrogens in the pdb file for the capping residues. So I
used pymol to add hydrogens to my pdb file. I then used this file with
charmm force field. However, pymol had added hydrogens everywhere and this
was different from the definition of the standard residues defined in the
.rtp file. I could not directly use -ignh because I needed the hydrogens for
the capping residues. So I created a file that contained the hydrogens on
the capping residues only. This resolved the error related to hydrogens.

Probably an easier and more reliable approach would simply be to create an
.hdb entry for your capping groups.

Maybe this is just showing up incorrectly in my mail client, but I wonder
if that CH3 is somehow misaligned and therefore not correctly identified. I
presume that you changed the residue name in the .rtp file accordingly? I
suppose the error message would be different (something like "residue not
found") but I just want to make sure. Mark's entry used NAC.
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17

Post by Sai Pooja
FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1 )
The error stated in the previous mail(quoted above) occurred when I chose
"none" for the both terminals or the carboxylic terminal option (using
-ter). It worked fine if I chose "none" at the N terminal and any other
option except "none" at the carboxylic acid terminal. So I chose "none" at N
terminal and some option randomly at the carboxylic acid terminal. As
expected, it adds a terminal at that end of the residue before my capping
residue which is something I DONT want. I

So does pdb2gmx somehow add the C-terminal cap after the carboxylate terminus?
havent been able to find a way around it. Interestingly, when I generate a

Post by Sai Pooja
pdb file using -q, and open that pdb file in pymol, I dont get the terminal
carboxylic acid that pdb2gmx gives in the .gro file.

So the cap is applied properly in that structure?
I am not sure how to correct this. One way would be to remove those

Post by Sai Pooja
entries from the final .gro and .top file but not sure if that would be
right.

This all sounds very fishy. This may be worth a bugzilla entry, but only
if you can build the structure in a very sound way, probably using .hdb
entries (or an appropriate all-atom structure, which you've yet to
demonstrate).
-Justin
Pooja

Post by Sai Pooja
Follow-up. It is easy to make it work. Just needed to be more
rigorous. Thank you.
It would be helpful if you describe what you mean. This error
message is new to me, and appears to reflect new mechanics in the
upcoming Gromacs release. If you describe what the problem was, how
you resolved it, what your pdb2gmx command line was, and anything
else that might be useful, that would likely help others solve this
issue in the future.
-Justin
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
I used -ter option and selected "none" for both terminal ends but I
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
I have used Mark's definitions for capping residues in the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00
1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00
0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00
2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00
1.60 FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
atom N not found in buiding block 1ACE while
combining tdb
and rtp
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb file as well?
What are you choosing as your termini when running pdb2gmx? It
should be "none," since by capping, you are not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au> <mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>,
Discussion list for
GROMACS users <gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
<mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
<mailto:gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>>>>

Post by Sai Pooja
I am sorry if I did not frame the question

correctly,
but putting
it very simply, is there a way to use capping residues
with the
charmm forcefield if the residues are --COCH3 and NHCH3?
Yes - you edit a copy of the .rtp file in your working
directory and
add whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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Justin A. Lemkul

2010-07-08 00:48:09 UTC

Permalink

Post by Sai Pooja
This probably is my ignorance but the error and the "bug" goes when I
replaced CBX with NAC everywhere.

I would suggest filing a bugzilla. I was able to reproduce your problem. If
nothing else, pdb2gmx should not be name-specific. Something very weird is
going on. More troubling, the topology that pdb2gmx generated for me with NAC
as the C-terminal cap had a broken net charge of +0.960 - it appears that
pdb2gmx is adding double hydrogens to the backbone amides - both H and HN.

With the impending release of Gromacs 4.5, this could be a very problematic bug.

-Justin

Post by Sai Pooja
On Wed, Jul 7, 2010 at 6:09 PM, Sai Pooja <saipooja at gmail.com
1. I have only added entries in the .rtp files. Do I need to add
them in .hdb and .tdb files too? Could I simply define a new
terminal in the aminoacids.c.tdb file?
*Initial PDB file*
ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1 C
ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1 O
ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
FR1 C
ATOM 4 HH31 ACE 1 13.138 -0.995 28.375 1.00 2.17
FR1 H
ATOM 5 HH32 ACE 1 11.856 0.230 28.537 1.00 2.17
FR1 H
ATOM 6 HH33 ACE 1 13.535 0.733 28.228 1.00 2.17
FR1 H
ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00 1.60
FR1 N
ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00 2.37
FR1 C
ATOM 9 C VAL 2 11.022 1.197 24.222 1.00 2.10
FR1 C
ATOM 10 O VAL 2 10.340 2.192 24.528 1.00 1.60
FR1 O
ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00 2.37
FR1 C
ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00 2.17
FR1 C
ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00 2.17
FR1 C
ATOM 14 H VAL 2 10.636 0.148 26.935 1.00 0.80
FR1 H
ATOM 15 N GLN 3 12.113 1.241 23.470 1.00 1.60
FR1
ATOM 16 H GLN 3 12.656 0.425 23.466 1.00 0.80
FR1
ATOM 17 CA GLN 3 12.533 2.509 22.812 1.00 2.37
FR1
ATOM 18 CB GLN 3 13.982 2.287 22.560 1.00 2.23
FR1
ATOM 19 CG GLN 3 14.807 3.474 22.166 1.00 2.23
FR1
ATOM 20 CD GLN 3 16.219 3.156 22.441 1.00 2.10
FR1
ATOM 21 OE1 GLN 3 16.635 2.341 23.295 1.00 1.60
FR1
ATOM 22 NE2 GLN 3 17.095 3.710 21.642 1.00 1.60
FR1
ATOM 23 HE21 GLN 3 18.031 3.421 21.665 1.00 0.80
FR1
ATOM 24 HE22 GLN 3 16.790 4.446 21.071 1.00 0.80
FR1
ATOM 25 C GLN 3 11.689 2.846 21.556 1.00 2.10
FR1
ATOM 26 O GLN 3 11.395 3.988 21.389 1.00 1.60
FR1
ATOM 27 N LEU 4 11.403 1.872 20.676 1.00 1.60
FR1
ATOM 28 H LEU 4 11.747 0.959 20.767 1.00 0.80
FR1
ATOM 29 CA LEU 4 10.606 2.121 19.473 1.00 2.37
FR1
ATOM 30 CB LEU 4 11.011 1.111 18.398 1.00 2.23
FR1
ATOM 31 CG LEU 4 12.501 1.073 18.020 1.00 2.37
FR1
ATOM 32 CD1 LEU 4 12.869 -0.185 17.207 1.00 2.17
FR1
ATOM 33 CD2 LEU 4 12.893 2.344 17.332 1.00 2.17
FR1
ATOM 34 C LEU 4 9.082 2.102 19.484 1.00 2.10
FR1
ATOM 35 O LEU 4 8.400 1.579 20.374 1.00 1.60
FR1
ATOM 36 N CBX 5 8.609 2.722 18.430 1.00 1.60
FR1
ATOM 37 H CBX 5 9.198 3.338 17.946 1.00 0.80
FR1
ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
FR1
ATOM 39 HH31 CBX 5 6.785 1.605 18.135 1.00 2.17
FR1 H
ATOM 40 HH32 CBX 5 7.178 2.732 16.814 1.00 2.17
FR1 H
ATOM 41 HH33 CBX 5 6.547 3.355 18.357 1.00 2.17
FR1
*Changes in .rtp file*
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ CBX ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
*command:*
pdb2gmx -f F1.pdb -q F1clean.pdb -nocmap -v -ss -ter -o work.gro -p
work.top
*.gro file from pdb2gmx*
1ACE CH3 1 1.278 -0.003 2.802
1ACE HH31 2 1.314 -0.100 2.838
1ACE HH32 3 1.186 0.023 2.854
1ACE HH33 4 1.354 0.073 2.823
1ACE C 5 1.253 -0.009 2.655
1ACE O 6 1.344 -0.021 2.570
2VAL N 7 1.125 -0.002 2.619
2VAL HN 8 1.064 0.015 2.694
2VAL CA 9 1.085 -0.021 2.485
2VAL HA 10 1.142 -0.094 2.447
2VAL CB 11 0.940 -0.068 2.471
2VAL HB 12 0.879 0.005 2.503
2VAL CG1 13 0.911 -0.095 2.327
2VAL HG11 14 0.817 -0.126 2.318
2VAL HG12 15 0.925 -0.012 2.274
2VAL HG13 16 0.973 -0.167 2.294
2VAL CG2 17 0.914 -0.195 2.555
2VAL HG21 18 0.819 -0.223 2.544
2VAL HG22 19 0.974 -0.268 2.523
2VAL HG23 20 0.932 -0.175 2.651
2VAL C 21 1.102 0.120 2.422
2VAL O 22 1.034 0.219 2.453
3GLN N 23 1.211 0.124 2.347
3GLN HN 24 1.266 0.043 2.347
3GLN CA 25 1.253 0.251 2.281
3GLN HA 26 1.240 0.331 2.340
3GLN CB 27 1.398 0.229 2.256
3GLN HB1 28 1.437 0.191 2.340
3GLN HB2 29 1.406 0.161 2.183
3GLN CG 30 1.481 0.347 2.217
3GLN HG1 31 1.469 0.367 2.119
3GLN HG2 32 1.453 0.428 2.270
3GLN CD 33 1.622 0.316 2.244
3GLN OE1 34 1.663 0.234 2.329
3GLN NE2 35 1.709 0.371 2.164
3GLN HE21 36 1.803 0.342 2.167
3GLN HE22 37 1.679 0.445 2.107
3GLN C 38 1.169 0.285 2.156
3GLN O 39 1.140 0.399 2.139
4LEU N 40 1.140 0.187 2.068
4LEU HN 41 1.175 0.096 2.077
4LEU CA 42 1.061 0.212 1.947
4LEU HA 43 1.085 0.309 1.937
4LEU CB 44 1.101 0.111 1.840
4LEU HB1 45 1.076 0.020 1.873
4LEU HB2 46 1.049 0.133 1.757
4LEU CG 47 1.250 0.107 1.802
4LEU HG 48 1.305 0.103 1.886
4LEU CD1 49 1.287 -0.019 1.721
4LEU HD11 50 1.384 -0.017 1.699
4LEU HD12 51 1.267 -0.100 1.775
4LEU HD13 52 1.234 -0.020 1.636
4LEU CD2 53 1.289 0.234 1.733
4LEU HD21 54 1.386 0.231 1.709
4LEU HD22 55 1.235 0.246 1.650
4LEU HD23 56 1.273 0.312 1.794
4LEU C 57 0.908 0.210 1.948
4LEU OT1 58 0.840 0.158 2.037
4LEU OT2 59 0.845 0.235 1.830
4LEU HT2 60 0.746 0.231 1.844
5CBX N 61 0.861 0.272 1.843
5CBX HN 62 0.920 0.334 1.795
5CBX CH3 63 0.718 0.259 1.789
5CBX HH31 64 0.678 0.161 1.814
5CBX HH32 65 0.718 0.273 1.681
5CBX HH33 66 0.655 0.336 1.836
1.14840 0.71270 1.21755
*PDB file from pdb2gmx using -q option*
TITLE Gromacs Runs On Most of All Computer Systems
MODEL 1
ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00 2.10
C
ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00 1.60
O
ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
C
ATOM 4 1HH3 ACE 1 13.138 -0.995 28.375 1.00 2.17
H
ATOM 5 2HH3 ACE 1 11.856 0.230 28.537 1.00 2.17
H
ATOM 6 3HH3 ACE 1 13.535 0.733 28.228 1.00 2.17
H
ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00 1.60
N
ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00 2.37
C
ATOM 9 C VAL 2 11.022 1.197 24.222 1.00 2.10
C
ATOM 10 O VAL 2 10.340 2.192 24.528 1.00 1.60
O
ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00 2.37
C
ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00 2.17
C
ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00 2.17
C
ATOM 14 H VAL 2 10.636 0.148 26.935 1.00 0.80
H
ATOM 15 N GLN 3 12.113 1.241 23.470 1.00 1.60
N
ATOM 16 H GLN 3 12.656 0.425 23.466 1.00 0.80
H
ATOM 17 CA GLN 3 12.533 2.509 22.812 1.00 2.37
C
ATOM 18 CB GLN 3 13.982 2.287 22.560 1.00 2.23
C
ATOM 19 CG GLN 3 14.807 3.474 22.166 1.00 2.23
C
ATOM 20 CD GLN 3 16.219 3.156 22.441 1.00 2.10
C
ATOM 21 OE1 GLN 3 16.635 2.341 23.295 1.00 1.60
O
ATOM 22 NE2 GLN 3 17.095 3.710 21.642 1.00 1.60
N
ATOM 23 1HE2 GLN 3 18.031 3.421 21.665 1.00 0.80
HE
ATOM 24 2HE2 GLN 3 16.790 4.446 21.071 1.00 0.80
HE
ATOM 25 C GLN 3 11.689 2.846 21.556 1.00 2.10
C
ATOM 26 O GLN 3 11.395 3.988 21.389 1.00 1.60
O
ATOM 27 N LEU 4 11.403 1.872 20.676 1.00 1.60
N
ATOM 28 H LEU 4 11.747 0.959 20.767 1.00 0.80
H
ATOM 29 CA LEU 4 10.606 2.121 19.473 1.00 2.37
C
ATOM 30 CB LEU 4 11.011 1.111 18.398 1.00 2.23
C
ATOM 31 CG LEU 4 12.501 1.073 18.020 1.00 2.37
C
ATOM 32 CD1 LEU 4 12.869 -0.185 17.207 1.00 2.17
C
ATOM 33 CD2 LEU 4 12.893 2.344 17.332 1.00 2.17
C
ATOM 34 C LEU 4 9.082 2.102 19.484 1.00 2.10
C
ATOM 35 O LEU 4 8.400 1.579 20.374 1.00 1.60
O
ATOM 36 N CBX 5 8.609 2.722 18.430 1.00 1.60
N
ATOM 37 H CBX 5 9.198 3.338 17.946 1.00 0.80
H
ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
C
ATOM 39 1HH3 CBX 5 6.785 1.605 18.135 1.00 2.17
H
ATOM 40 2HH3 CBX 5 7.178 2.732 16.814 1.00 2.17
H
ATOM 41 3HH3 CBX 5 6.547 3.355 18.357 1.00 2.17
H
TER
ENDMDL
These files were generated using the option -COOH for C terminal.
*However, if "none" is chosen, I get the error:*
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.
Pooja
On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul <jalemkul at vt.edu
I checked again and the error does not go. Please read the
steps below.
The pdb file I started off with did not have any hydrogens.
However, the way I had specified the capping residues in the
.rtp file (SEE MARK'S MAIL), I had to specify hydrogens in
the pdb file for the capping residues. So I used pymol to
add hydrogens to my pdb file. I then used this file with
charmm force field. However, pymol had added hydrogens
everywhere and this was different from the definition of the
standard residues defined in the .rtp file. I could not
directly use -ignh because I needed the hydrogens for the
capping residues. So I created a file that contained the
hydrogens on the capping residues only. This resolved the
error related to hydrogens.
Probably an easier and more reliable approach would simply be to
create an .hdb entry for your capping groups.
Error-from previous mail-NOT RESOLVED
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please
check the
GROMACS
I have used Mark's definitions for capping residues in
the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430
1.00 1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946
1.00 0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895
1.00 2.17 FR1
Maybe this is just showing up incorrectly in my mail client, but
I wonder if that CH3 is somehow misaligned and therefore not
correctly identified. I presume that you changed the residue
name in the .rtp file accordingly? I suppose the error message
would be different (something like "residue not found") but I
just want to make sure. Mark's entry used NAC.
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022
1.00 2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546
1.00 2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696
1.00 1.60 FR1 )
The error stated in the previous mail(quoted above) occurred
when I chose "none" for the both terminals or the carboxylic
terminal option (using -ter). It worked fine if I chose
"none" at the N terminal and any other option except "none"
at the carboxylic acid terminal. So I chose "none" at N
terminal and some option randomly at the carboxylic acid
terminal. As expected, it adds a terminal at that end of the
residue before my capping residue which is something I DONT
want. I
So does pdb2gmx somehow add the C-terminal cap after the
carboxylate terminus?
havent been able to find a way around it. Interestingly,
when I generate a pdb file using -q, and open that pdb file
in pymol, I dont get the terminal carboxylic acid that
pdb2gmx gives in the .gro file.
So the cap is applied properly in that structure?
I am not sure how to correct this. One way would be to
remove those entries from the final .gro and .top file but
not sure if that would be right.
This all sounds very fishy. This may be worth a bugzilla entry,
but only if you can build the structure in a very sound way,
probably using .hdb entries (or an appropriate all-atom
structure, which you've yet to demonstrate).
-Justin
Pooja
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Follow-up. It is easy to make it work. Just needed to
be more
rigorous. Thank you.
It would be helpful if you describe what you mean. This error
message is new to me, and appears to reflect new
mechanics in the
upcoming Gromacs release. If you describe what the
problem was, how
you resolved it, what your pdb2gmx command line was, and
anything
else that might be useful, that would likely help others
solve this
issue in the future.
-Justin
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja
<saipooja at gmail.com <mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
I used -ter option and selected "none" for both
terminal ends
but I
There is a dangling bond at at least one of the
terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please
check the
GROMACS
I have used Mark's definitions for capping
residues in the
rtp file.
In the pdb file, this is what the capping residues
ATOM 33 N CBX 5 8.609 2.722
18.430 1.00
1.60 FR1
ATOM 34 H CBX 5 9.198 3.338
17.946 1.00
0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594
17.895 1.00
2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027
28.022 1.00
2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094
26.546 1.00
2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213
25.696 1.00
1.60 FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
atom N not found in buiding block 1ACE while
combining tdb
and rtp
For more information and tips for
troubleshooting, please
check the GROMACS
website at
http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb
file as well?
What are you choosing as your termini when running
pdb2gmx? It
should be "none," since by capping, you are
not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu
<mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
<mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
<mailto:jalemkul at vt.edu
<mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
<mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>,
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Post by Sai Pooja
I am sorry if I did not frame the

Justin A. Lemkul

2010-07-08 01:11:59 UTC

Permalink

As a follow-up, it appears that there are several problems with the CHARMM
implementation. I will file a bugzilla with a few other things I found. There
are a number of errors in the aminoacids.rtp file that cause problems. Most of
all, I can't even get pdb2gmx to generate a CHARMM topology for lysozyme. If
that fails, then we're in trouble :)

-Justin

Post by Justin A. Lemkul

Post by Sai Pooja
This probably is my ignorance but the error and the "bug" goes when I
replaced CBX with NAC everywhere.

I would suggest filing a bugzilla. I was able to reproduce your
problem. If nothing else, pdb2gmx should not be name-specific.
Something very weird is going on. More troubling, the topology that
pdb2gmx generated for me with NAC as the C-terminal cap had a broken net
charge of +0.960 - it appears that pdb2gmx is adding double hydrogens to
the backbone amides - both H and HN.
With the impending release of Gromacs 4.5, this could be a very problematic bug.
-Justin

Post by Sai Pooja
On Wed, Jul 7, 2010 at 6:09 PM, Sai Pooja <saipooja at gmail.com
1. I have only added entries in the .rtp files. Do I need to add
them in .hdb and .tdb files too? Could I simply define a new
terminal in the aminoacids.c.tdb file?
*Initial PDB file*
ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00
2.10 FR1 C
ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00
1.60 FR1 O
ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 FR1 C
ATOM 4 HH31 ACE 1 13.138 -0.995 28.375 1.00
2.17 FR1 H
ATOM 5 HH32 ACE 1 11.856 0.230 28.537 1.00
2.17 FR1 H
ATOM 6 HH33 ACE 1 13.535 0.733 28.228 1.00
2.17 FR1 H
ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00
1.60 FR1 N
ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00
2.37 FR1 C
ATOM 9 C VAL 2 11.022 1.197 24.222 1.00
2.10 FR1 C
ATOM 10 O VAL 2 10.340 2.192 24.528 1.00
1.60 FR1 O
ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00
2.37 FR1 C
ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00
2.17 FR1 C
ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00
2.17 FR1 C
ATOM 14 H VAL 2 10.636 0.148 26.935 1.00
0.80 FR1 H
ATOM 15 N GLN 3 12.113 1.241 23.470 1.00
1.60 FR1 ATOM 16 H GLN 3 12.656 0.425
23.466 1.00 0.80 FR1 ATOM 17 CA GLN 3
12.533 2.509 22.812 1.00 2.37 FR1 ATOM 18 CB
GLN 3 13.982 2.287 22.560 1.00 2.23 FR1
ATOM 19 CG GLN 3 14.807 3.474 22.166 1.00 2.23
FR1 ATOM 20 CD GLN 3 16.219 3.156 22.441
1.00 2.10 FR1 ATOM 21 OE1 GLN 3 16.635
2.341 23.295 1.00 1.60 FR1 ATOM 22 NE2 GLN
3 17.095 3.710 21.642 1.00 1.60 FR1 ATOM 23
HE21 GLN 3 18.031 3.421 21.665 1.00 0.80 FR1
ATOM 24 HE22 GLN 3 16.790 4.446 21.071 1.00 0.80
FR1 ATOM 25 C GLN 3 11.689 2.846 21.556
1.00 2.10 FR1 ATOM 26 O GLN 3 11.395
3.988 21.389 1.00 1.60 FR1 ATOM 27 N LEU
4 11.403 1.872 20.676 1.00 1.60 FR1 ATOM 28
H LEU 4 11.747 0.959 20.767 1.00 0.80 FR1
ATOM 29 CA LEU 4 10.606 2.121 19.473 1.00 2.37
FR1 ATOM 30 CB LEU 4 11.011 1.111 18.398
1.00 2.23 FR1 ATOM 31 CG LEU 4 12.501
1.073 18.020 1.00 2.37 FR1 ATOM 32 CD1 LEU
4 12.869 -0.185 17.207 1.00 2.17 FR1 ATOM 33
CD2 LEU 4 12.893 2.344 17.332 1.00 2.17 FR1
ATOM 34 C LEU 4 9.082 2.102 19.484 1.00 2.10
FR1 ATOM 35 O LEU 4 8.400 1.579 20.374
1.00 1.60 FR1 ATOM 36 N CBX 5 8.609
2.722 18.430 1.00 1.60 FR1
ATOM 37 H CBX 5 9.198 3.338 17.946 1.00
0.80 FR1
ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 FR1
ATOM 39 HH31 CBX 5 6.785 1.605 18.135 1.00
2.17 FR1 H
ATOM 40 HH32 CBX 5 7.178 2.732 16.814 1.00
2.17 FR1 H
ATOM 41 HH33 CBX 5 6.547 3.355 18.357 1.00
2.17 FR1
*Changes in .rtp file*
[ ACE ] [ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ CBX ]
[ atoms ]
N NH1 -0.470 1 HN H
0.310 1 CH3 CT3 -0.110 1 HH31
HA 0.090 1 HH32 HA 0.090 1
HH33 HA 0.090 1 [ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
*command:*
pdb2gmx -f F1.pdb -q F1clean.pdb -nocmap -v -ss -ter -o work.gro -p
work.top
*.gro file from pdb2gmx*
1ACE CH3 1 1.278 -0.003 2.802
1ACE HH31 2 1.314 -0.100 2.838
1ACE HH32 3 1.186 0.023 2.854
1ACE HH33 4 1.354 0.073 2.823
1ACE C 5 1.253 -0.009 2.655
1ACE O 6 1.344 -0.021 2.570
2VAL N 7 1.125 -0.002 2.619
2VAL HN 8 1.064 0.015 2.694
2VAL CA 9 1.085 -0.021 2.485
2VAL HA 10 1.142 -0.094 2.447
2VAL CB 11 0.940 -0.068 2.471
2VAL HB 12 0.879 0.005 2.503
2VAL CG1 13 0.911 -0.095 2.327
2VAL HG11 14 0.817 -0.126 2.318
2VAL HG12 15 0.925 -0.012 2.274
2VAL HG13 16 0.973 -0.167 2.294
2VAL CG2 17 0.914 -0.195 2.555
2VAL HG21 18 0.819 -0.223 2.544
2VAL HG22 19 0.974 -0.268 2.523
2VAL HG23 20 0.932 -0.175 2.651
2VAL C 21 1.102 0.120 2.422
2VAL O 22 1.034 0.219 2.453
3GLN N 23 1.211 0.124 2.347
3GLN HN 24 1.266 0.043 2.347
3GLN CA 25 1.253 0.251 2.281
3GLN HA 26 1.240 0.331 2.340
3GLN CB 27 1.398 0.229 2.256
3GLN HB1 28 1.437 0.191 2.340
3GLN HB2 29 1.406 0.161 2.183
3GLN CG 30 1.481 0.347 2.217
3GLN HG1 31 1.469 0.367 2.119
3GLN HG2 32 1.453 0.428 2.270
3GLN CD 33 1.622 0.316 2.244
3GLN OE1 34 1.663 0.234 2.329
3GLN NE2 35 1.709 0.371 2.164
3GLN HE21 36 1.803 0.342 2.167
3GLN HE22 37 1.679 0.445 2.107
3GLN C 38 1.169 0.285 2.156
3GLN O 39 1.140 0.399 2.139
4LEU N 40 1.140 0.187 2.068
4LEU HN 41 1.175 0.096 2.077
4LEU CA 42 1.061 0.212 1.947
4LEU HA 43 1.085 0.309 1.937
4LEU CB 44 1.101 0.111 1.840
4LEU HB1 45 1.076 0.020 1.873
4LEU HB2 46 1.049 0.133 1.757
4LEU CG 47 1.250 0.107 1.802
4LEU HG 48 1.305 0.103 1.886
4LEU CD1 49 1.287 -0.019 1.721
4LEU HD11 50 1.384 -0.017 1.699
4LEU HD12 51 1.267 -0.100 1.775
4LEU HD13 52 1.234 -0.020 1.636
4LEU CD2 53 1.289 0.234 1.733
4LEU HD21 54 1.386 0.231 1.709
4LEU HD22 55 1.235 0.246 1.650
4LEU HD23 56 1.273 0.312 1.794
4LEU C 57 0.908 0.210 1.948
4LEU OT1 58 0.840 0.158 2.037
4LEU OT2 59 0.845 0.235 1.830
4LEU HT2 60 0.746 0.231 1.844
5CBX N 61 0.861 0.272 1.843
5CBX HN 62 0.920 0.334 1.795
5CBX CH3 63 0.718 0.259 1.789
5CBX HH31 64 0.678 0.161 1.814
5CBX HH32 65 0.718 0.273 1.681
5CBX HH33 66 0.655 0.336 1.836
1.14840 0.71270 1.21755
*PDB file from pdb2gmx using -q option*
TITLE Gromacs Runs On Most of All Computer Systems
MODEL 1
ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00
2.10 C
ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00
1.60 O
ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 C
ATOM 4 1HH3 ACE 1 13.138 -0.995 28.375 1.00
2.17 H
ATOM 5 2HH3 ACE 1 11.856 0.230 28.537 1.00
2.17 H
ATOM 6 3HH3 ACE 1 13.535 0.733 28.228 1.00
2.17 H
ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00
1.60 N
ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00
2.37 C
ATOM 9 C VAL 2 11.022 1.197 24.222 1.00
2.10 C
ATOM 10 O VAL 2 10.340 2.192 24.528 1.00
1.60 O
ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00
2.37 C
ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00
2.17 C
ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00
2.17 C
ATOM 14 H VAL 2 10.636 0.148 26.935 1.00
0.80 H
ATOM 15 N GLN 3 12.113 1.241 23.470 1.00
1.60 N
ATOM 16 H GLN 3 12.656 0.425 23.466 1.00
0.80 H
ATOM 17 CA GLN 3 12.533 2.509 22.812 1.00
2.37 C
ATOM 18 CB GLN 3 13.982 2.287 22.560 1.00
2.23 C
ATOM 19 CG GLN 3 14.807 3.474 22.166 1.00
2.23 C
ATOM 20 CD GLN 3 16.219 3.156 22.441 1.00
2.10 C
ATOM 21 OE1 GLN 3 16.635 2.341 23.295 1.00
1.60 O
ATOM 22 NE2 GLN 3 17.095 3.710 21.642 1.00
1.60 N
ATOM 23 1HE2 GLN 3 18.031 3.421 21.665 1.00
0.80 HE
ATOM 24 2HE2 GLN 3 16.790 4.446 21.071 1.00
0.80 HE
ATOM 25 C GLN 3 11.689 2.846 21.556 1.00
2.10 C
ATOM 26 O GLN 3 11.395 3.988 21.389 1.00
1.60 O
ATOM 27 N LEU 4 11.403 1.872 20.676 1.00
1.60 N
ATOM 28 H LEU 4 11.747 0.959 20.767 1.00
0.80 H
ATOM 29 CA LEU 4 10.606 2.121 19.473 1.00
2.37 C
ATOM 30 CB LEU 4 11.011 1.111 18.398 1.00
2.23 C
ATOM 31 CG LEU 4 12.501 1.073 18.020 1.00
2.37 C
ATOM 32 CD1 LEU 4 12.869 -0.185 17.207 1.00
2.17 C
ATOM 33 CD2 LEU 4 12.893 2.344 17.332 1.00
2.17 C
ATOM 34 C LEU 4 9.082 2.102 19.484 1.00
2.10 C
ATOM 35 O LEU 4 8.400 1.579 20.374 1.00
1.60 O
ATOM 36 N CBX 5 8.609 2.722 18.430 1.00
1.60 N
ATOM 37 H CBX 5 9.198 3.338 17.946 1.00
0.80 H
ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 C
ATOM 39 1HH3 CBX 5 6.785 1.605 18.135 1.00
2.17 H
ATOM 40 2HH3 CBX 5 7.178 2.732 16.814 1.00
2.17 H
ATOM 41 3HH3 CBX 5 6.547 3.355 18.357 1.00
2.17 H
TER
ENDMDL
These files were generated using the option -COOH for C terminal.
*However, if "none" is chosen, I get the error:*
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
I have used Mark's definitions for capping residues in the rtp file.
Pooja
On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul <jalemkul at vt.edu
I checked again and the error does not go. Please read the
steps below.
The pdb file I started off with did not have any hydrogens.
However, the way I had specified the capping residues in the
.rtp file (SEE MARK'S MAIL), I had to specify hydrogens in
the pdb file for the capping residues. So I used pymol to
add hydrogens to my pdb file. I then used this file with
charmm force field. However, pymol had added hydrogens
everywhere and this was different from the definition of the
standard residues defined in the .rtp file. I could not
directly use -ignh because I needed the hydrogens for the
capping residues. So I created a file that contained the
hydrogens on the capping residues only. This resolved the
error related to hydrogens.
Probably an easier and more reliable approach would simply be to
create an .hdb entry for your capping groups.
Error-from previous mail-NOT RESOLVED
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please
check the
GROMACS
I have used Mark's definitions for capping residues in
the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430
1.00 1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946
1.00 0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895
1.00 2.17 FR1
Maybe this is just showing up incorrectly in my mail client, but
I wonder if that CH3 is somehow misaligned and therefore not
correctly identified. I presume that you changed the residue
name in the .rtp file accordingly? I suppose the error message
would be different (something like "residue not found") but I
just want to make sure. Mark's entry used NAC.
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022
1.00 2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546
1.00 2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696
1.00 1.60 FR1 )
The error stated in the previous mail(quoted above) occurred
when I chose "none" for the both terminals or the carboxylic
terminal option (using -ter). It worked fine if I chose
"none" at the N terminal and any other option except "none"
at the carboxylic acid terminal. So I chose "none" at N
terminal and some option randomly at the carboxylic acid
terminal. As expected, it adds a terminal at that end of the
residue before my capping residue which is something I DONT
want. I
So does pdb2gmx somehow add the C-terminal cap after the
carboxylate terminus?
havent been able to find a way around it. Interestingly,
when I generate a pdb file using -q, and open that pdb file
in pymol, I dont get the terminal carboxylic acid that
pdb2gmx gives in the .gro file.
So the cap is applied properly in that structure?
I am not sure how to correct this. One way would be to
remove those entries from the final .gro and .top file but
not sure if that would be right.
This all sounds very fishy. This may be worth a bugzilla entry,
but only if you can build the structure in a very sound way,
probably using .hdb entries (or an appropriate all-atom
structure, which you've yet to demonstrate).
-Justin
Pooja
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Follow-up. It is easy to make it work. Just needed to
be more
rigorous. Thank you.
It would be helpful if you describe what you mean. This error
message is new to me, and appears to reflect new
mechanics in the
upcoming Gromacs release. If you describe what the
problem was, how
you resolved it, what your pdb2gmx command line was, and
anything
else that might be useful, that would likely help others
solve this
issue in the future.
-Justin
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja
<saipooja at gmail.com <mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
I used -ter option and selected "none" for both
terminal ends
but I
There is a dangling bond at at least one of the
terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting,
please
check the
GROMACS
I have used Mark's definitions for capping
residues in the
rtp file.
In the pdb file, this is what the capping residues
ATOM 33 N CBX 5 8.609 2.722
18.430 1.00
1.60 FR1
ATOM 34 H CBX 5 9.198 3.338
17.946 1.00
0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594
17.895 1.00
2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027
28.022 1.00
2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094
26.546 1.00
2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213
25.696 1.00
1.60 FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Thanks Marks. I tried it but this is what
atom N not found in buiding block 1ACE while
combining tdb
and rtp
For more information and tips for
troubleshooting, please
check the GROMACS
website at
http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb
file as well?
What are you choosing as your termini when running
pdb2gmx? It
should be "none," since by capping, you are
not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu
<mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
<mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
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<mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>,
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Post by Sai Pooja
I am sorry if I did not frame the

Justin A. Lemkul

2010-07-08 02:14:17 UTC

Permalink

Hi Justin,
I do not have the problem of extra hydrogens or a net charge on the NAC
group.

The net charge is not on NAC, it's on the entire peptide. If you're not seeing
it, that makes the bug even more troubling, since it's sporadic. Are you using
the latest git version, or an older one? If it's older, that may help track
down the code change that is causing problems.

In relation to the other bugs you have mentioned, would it be a good
idea to start a project with this git version of gromacs? The topology
file I have now looks fine but I may be missing certain irregularities.
Is there a good way to check?

I would never recommend using a git version for production work. It is under
continual development (thanks to the hard work of the developers!) and as such,
small (or large) bugs may get occasionally introduced, or new features added or
modified. I would only suggest using a git version for actual data collection
if it fixes a specific bug that was a problem for you and the git version fixes
it and is stable.

As far as checking, I have no idea. The test suite needs to be developed
further before there is a useful set of tools for validating a GROMACS installation.

Is there another safe way to use the charmm forcefield with
gromacs(without gromacs)?

Supposedly the CHARMM implementation in GROMACS is stable, but maybe changes in
the code have given rise to the bugs I'm suspecting. I can't even get a
topology for lysozyme; there are a host of errors which are concerning to me.

Otherwise use the CHARMM program, or even NAMD.

-Justin

Pooja
On Wed, Jul 7, 2010 at 8:48 PM, Justin A. Lemkul <jalemkul at vt.edu
This probably is my ignorance but the error and the "bug" goes
when I replaced CBX with NAC everywhere.
I would suggest filing a bugzilla. I was able to reproduce your
problem. If nothing else, pdb2gmx should not be name-specific.
Something very weird is going on. More troubling, the topology
that pdb2gmx generated for me with NAC as the C-terminal cap had a
broken net charge of +0.960 - it appears that pdb2gmx is adding
double hydrogens to the backbone amides - both H and HN.
With the impending release of Gromacs 4.5, this could be a very problematic bug.
-Justin
On Wed, Jul 7, 2010 at 6:09 PM, Sai Pooja <saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
1. I have only added entries in the .rtp files. Do I need to add
them in .hdb and .tdb files too? Could I simply define a new
terminal in the aminoacids.c.tdb file?
*Initial PDB file*
ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00
2.10 FR1 C
ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00
1.60 FR1 O
ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 FR1 C
ATOM 4 HH31 ACE 1 13.138 -0.995 28.375 1.00
2.17 FR1 H
ATOM 5 HH32 ACE 1 11.856 0.230 28.537 1.00
2.17 FR1 H
ATOM 6 HH33 ACE 1 13.535 0.733 28.228 1.00
2.17 FR1 H
ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00
1.60 FR1 N
ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00
2.37 FR1 C
ATOM 9 C VAL 2 11.022 1.197 24.222 1.00
2.10 FR1 C
ATOM 10 O VAL 2 10.340 2.192 24.528 1.00
1.60 FR1 O
ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00
2.37 FR1 C
ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00
2.17 FR1 C
ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00
2.17 FR1 C
ATOM 14 H VAL 2 10.636 0.148 26.935 1.00
0.80 FR1 H
ATOM 15 N GLN 3 12.113 1.241 23.470 1.00
1.60 FR1 ATOM 16 H GLN 3 12.656
0.425 23.466 1.00 0.80 FR1 ATOM 17 CA GLN
3 12.533 2.509 22.812 1.00 2.37 FR1 ATOM
18 CB GLN 3 13.982 2.287 22.560 1.00 2.23
FR1 ATOM 19 CG GLN 3 14.807 3.474
22.166 1.00 2.23 FR1 ATOM 20 CD GLN 3
16.219 3.156 22.441 1.00 2.10 FR1 ATOM
21 OE1 GLN 3 16.635 2.341 23.295 1.00 1.60
FR1 ATOM 22 NE2 GLN 3 17.095 3.710 21.642
1.00 1.60 FR1 ATOM 23 HE21 GLN 3
18.031 3.421 21.665 1.00 0.80 FR1 ATOM 24
HE22 GLN 3 16.790 4.446 21.071 1.00 0.80
FR1 ATOM 25 C GLN 3 11.689 2.846 21.556
1.00 2.10 FR1 ATOM 26 O GLN 3
11.395 3.988 21.389 1.00 1.60 FR1 ATOM 27
N LEU 4 11.403 1.872 20.676 1.00 1.60
FR1 ATOM 28 H LEU 4 11.747 0.959 20.767
1.00 0.80 FR1 ATOM 29 CA LEU 4
10.606 2.121 19.473 1.00 2.37 FR1 ATOM 30
CB LEU 4 11.011 1.111 18.398 1.00 2.23
FR1 ATOM 31 CG LEU 4 12.501 1.073 18.020
1.00 2.37 FR1 ATOM 32 CD1 LEU 4
12.869 -0.185 17.207 1.00 2.17 FR1 ATOM 33
CD2 LEU 4 12.893 2.344 17.332 1.00 2.17
FR1 ATOM 34 C LEU 4 9.082 2.102 19.484
1.00 2.10 FR1 ATOM 35 O LEU 4
8.400 1.579 20.374 1.00 1.60 FR1 ATOM 36 N
CBX 5 8.609 2.722 18.430 1.00 1.60 FR1
ATOM 37 H CBX 5 9.198 3.338 17.946 1.00
0.80 FR1
ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 FR1
ATOM 39 HH31 CBX 5 6.785 1.605 18.135 1.00
2.17 FR1 H
ATOM 40 HH32 CBX 5 7.178 2.732 16.814 1.00
2.17 FR1 H
ATOM 41 HH33 CBX 5 6.547 3.355 18.357 1.00
2.17 FR1
*Changes in .rtp file*
[ ACE ] [ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ CBX ]
[ atoms ]
N NH1 -0.470 1 HN H
0.310 1 CH3 CT3 -0.110 1 HH31
HA 0.090 1 HH32 HA 0.090 1
HH33 HA 0.090 1 [ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
*command:*
pdb2gmx -f F1.pdb -q F1clean.pdb -nocmap -v -ss -ter -o work.gro -p
work.top
*.gro file from pdb2gmx*
1ACE CH3 1 1.278 -0.003 2.802
1ACE HH31 2 1.314 -0.100 2.838
1ACE HH32 3 1.186 0.023 2.854
1ACE HH33 4 1.354 0.073 2.823
1ACE C 5 1.253 -0.009 2.655
1ACE O 6 1.344 -0.021 2.570
2VAL N 7 1.125 -0.002 2.619
2VAL HN 8 1.064 0.015 2.694
2VAL CA 9 1.085 -0.021 2.485
2VAL HA 10 1.142 -0.094 2.447
2VAL CB 11 0.940 -0.068 2.471
2VAL HB 12 0.879 0.005 2.503
2VAL CG1 13 0.911 -0.095 2.327
2VAL HG11 14 0.817 -0.126 2.318
2VAL HG12 15 0.925 -0.012 2.274
2VAL HG13 16 0.973 -0.167 2.294
2VAL CG2 17 0.914 -0.195 2.555
2VAL HG21 18 0.819 -0.223 2.544
2VAL HG22 19 0.974 -0.268 2.523
2VAL HG23 20 0.932 -0.175 2.651
2VAL C 21 1.102 0.120 2.422
2VAL O 22 1.034 0.219 2.453
3GLN N 23 1.211 0.124 2.347
3GLN HN 24 1.266 0.043 2.347
3GLN CA 25 1.253 0.251 2.281
3GLN HA 26 1.240 0.331 2.340
3GLN CB 27 1.398 0.229 2.256
3GLN HB1 28 1.437 0.191 2.340
3GLN HB2 29 1.406 0.161 2.183
3GLN CG 30 1.481 0.347 2.217
3GLN HG1 31 1.469 0.367 2.119
3GLN HG2 32 1.453 0.428 2.270
3GLN CD 33 1.622 0.316 2.244
3GLN OE1 34 1.663 0.234 2.329
3GLN NE2 35 1.709 0.371 2.164
3GLN HE21 36 1.803 0.342 2.167
3GLN HE22 37 1.679 0.445 2.107
3GLN C 38 1.169 0.285 2.156
3GLN O 39 1.140 0.399 2.139
4LEU N 40 1.140 0.187 2.068
4LEU HN 41 1.175 0.096 2.077
4LEU CA 42 1.061 0.212 1.947
4LEU HA 43 1.085 0.309 1.937
4LEU CB 44 1.101 0.111 1.840
4LEU HB1 45 1.076 0.020 1.873
4LEU HB2 46 1.049 0.133 1.757
4LEU CG 47 1.250 0.107 1.802
4LEU HG 48 1.305 0.103 1.886
4LEU CD1 49 1.287 -0.019 1.721
4LEU HD11 50 1.384 -0.017 1.699
4LEU HD12 51 1.267 -0.100 1.775
4LEU HD13 52 1.234 -0.020 1.636
4LEU CD2 53 1.289 0.234 1.733
4LEU HD21 54 1.386 0.231 1.709
4LEU HD22 55 1.235 0.246 1.650
4LEU HD23 56 1.273 0.312 1.794
4LEU C 57 0.908 0.210 1.948
4LEU OT1 58 0.840 0.158 2.037
4LEU OT2 59 0.845 0.235 1.830
4LEU HT2 60 0.746 0.231 1.844
5CBX N 61 0.861 0.272 1.843
5CBX HN 62 0.920 0.334 1.795
5CBX CH3 63 0.718 0.259 1.789
5CBX HH31 64 0.678 0.161 1.814
5CBX HH32 65 0.718 0.273 1.681
5CBX HH33 66 0.655 0.336 1.836
1.14840 0.71270 1.21755
*PDB file from pdb2gmx using -q option*
TITLE Gromacs Runs On Most of All Computer Systems
MODEL 1
ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00
2.10 C
ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00
1.60 O
ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 C
ATOM 4 1HH3 ACE 1 13.138 -0.995 28.375 1.00
2.17 H
ATOM 5 2HH3 ACE 1 11.856 0.230 28.537 1.00
2.17 H
ATOM 6 3HH3 ACE 1 13.535 0.733 28.228 1.00
2.17 H
ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00
1.60 N
ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00
2.37 C
ATOM 9 C VAL 2 11.022 1.197 24.222 1.00
2.10 C
ATOM 10 O VAL 2 10.340 2.192 24.528 1.00
1.60 O
ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00
2.37 C
ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00
2.17 C
ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00
2.17 C
ATOM 14 H VAL 2 10.636 0.148 26.935 1.00
0.80 H
ATOM 15 N GLN 3 12.113 1.241 23.470 1.00
1.60 N
ATOM 16 H GLN 3 12.656 0.425 23.466 1.00
0.80 H
ATOM 17 CA GLN 3 12.533 2.509 22.812 1.00
2.37 C
ATOM 18 CB GLN 3 13.982 2.287 22.560 1.00
2.23 C
ATOM 19 CG GLN 3 14.807 3.474 22.166 1.00
2.23 C
ATOM 20 CD GLN 3 16.219 3.156 22.441 1.00
2.10 C
ATOM 21 OE1 GLN 3 16.635 2.341 23.295 1.00
1.60 O
ATOM 22 NE2 GLN 3 17.095 3.710 21.642 1.00
1.60 N
ATOM 23 1HE2 GLN 3 18.031 3.421 21.665 1.00
0.80 HE
ATOM 24 2HE2 GLN 3 16.790 4.446 21.071 1.00
0.80 HE
ATOM 25 C GLN 3 11.689 2.846 21.556 1.00
2.10 C
ATOM 26 O GLN 3 11.395 3.988 21.389 1.00
1.60 O
ATOM 27 N LEU 4 11.403 1.872 20.676 1.00
1.60 N
ATOM 28 H LEU 4 11.747 0.959 20.767 1.00
0.80 H
ATOM 29 CA LEU 4 10.606 2.121 19.473 1.00
2.37 C
ATOM 30 CB LEU 4 11.011 1.111 18.398 1.00
2.23 C
ATOM 31 CG LEU 4 12.501 1.073 18.020 1.00
2.37 C
ATOM 32 CD1 LEU 4 12.869 -0.185 17.207 1.00
2.17 C
ATOM 33 CD2 LEU 4 12.893 2.344 17.332 1.00
2.17 C
ATOM 34 C LEU 4 9.082 2.102 19.484 1.00
2.10 C
ATOM 35 O LEU 4 8.400 1.579 20.374 1.00
1.60 O
ATOM 36 N CBX 5 8.609 2.722 18.430 1.00
1.60 N
ATOM 37 H CBX 5 9.198 3.338 17.946 1.00
0.80 H
ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 C
ATOM 39 1HH3 CBX 5 6.785 1.605 18.135 1.00
2.17 H
ATOM 40 2HH3 CBX 5 7.178 2.732 16.814 1.00
2.17 H
ATOM 41 3HH3 CBX 5 6.547 3.355 18.357 1.00
2.17 H
TER
ENDMDL
These files were generated using the option -COOH for C terminal.
*However, if "none" is chosen, I get the error:*
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
I have used Mark's definitions for capping residues in the rtp file.
Pooja
On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
I checked again and the error does not go. Please read the
steps below.
The pdb file I started off with did not have any hydrogens.
However, the way I had specified the capping residues in the
.rtp file (SEE MARK'S MAIL), I had to specify hydrogens in
the pdb file for the capping residues. So I used pymol to
add hydrogens to my pdb file. I then used this file with
charmm force field. However, pymol had added hydrogens
everywhere and this was different from the definition of the
standard residues defined in the .rtp file. I could not
directly use -ignh because I needed the hydrogens for the
capping residues. So I created a file that contained the
hydrogens on the capping residues only. This resolved the
error related to hydrogens.
Probably an easier and more reliable approach would simply be to
create an .hdb entry for your capping groups.
Error-from previous mail-NOT RESOLVED
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please
check the
GROMACS
I have used Mark's definitions for capping residues in
the rtp file.
ATOM 33 N CBX 5 8.609 2.722 18.430
1.00 1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946
1.00 0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895
1.00 2.17 FR1
Maybe this is just showing up incorrectly in my mail client, but
I wonder if that CH3 is somehow misaligned and therefore not
correctly identified. I presume that you changed the residue
name in the .rtp file accordingly? I suppose the error message
would be different (something like "residue not found") but I
just want to make sure. Mark's entry used NAC.
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022
1.00 2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546
1.00 2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696
1.00 1.60 FR1 )
The error stated in the previous mail(quoted above) occurred
when I chose "none" for the both terminals or the carboxylic
terminal option (using -ter). It worked fine if I chose
"none" at the N terminal and any other option except "none"
at the carboxylic acid terminal. So I chose "none" at N
terminal and some option randomly at the carboxylic acid
terminal. As expected, it adds a terminal at that end of the
residue before my capping residue which is something I DONT
want. I
So does pdb2gmx somehow add the C-terminal cap after the
carboxylate terminus?
havent been able to find a way around it. Interestingly,
when I generate a pdb file using -q, and open that pdb file
in pymol, I dont get the terminal carboxylic acid that
pdb2gmx gives in the .gro file.
So the cap is applied properly in that structure?
I am not sure how to correct this. One way would be to
remove those entries from the final .gro and .top file but
not sure if that would be right.
This all sounds very fishy. This may be worth a bugzilla entry,
but only if you can build the structure in a very sound way,
probably using .hdb entries (or an appropriate all-atom
structure, which you've yet to demonstrate).
-Justin
Pooja
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Follow-up. It is easy to make it work. Just needed to
be more
rigorous. Thank you.
It would be helpful if you describe what you mean.
This
error
message is new to me, and appears to reflect new
mechanics in the
upcoming Gromacs release. If you describe what the
problem was, how
you resolved it, what your pdb2gmx command line was, and
anything
else that might be useful, that would likely help others
solve this
issue in the future.
-Justin
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja
<saipooja at gmail.com <mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
I used -ter option and selected "none" for both
terminal ends
but I
There is a dangling bond at at least one of the
terminal ends.
Select a proper terminal entry.
For more information and tips for
troubleshooting,
please
check the
GROMACS
I have used Mark's definitions for capping
residues in the
rtp file.
In the pdb file, this is what the capping residues
ATOM 33 N CBX 5 8.609 2.722
18.430 1.00
1.60 FR1
ATOM 34 H CBX 5 9.198 3.338
17.946 1.00
0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594
17.895 1.00
2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027
28.022 1.00
2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094
26.546 1.00
2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213
25.696 1.00
1.60 FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
<mailto:jalemkul at vt.edu
<mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
<mailto:jalemkul at vt.edu>>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Thanks Marks. I tried it but this
is what
atom N not found in buiding block 1ACE while
combining tdb
and rtp
For more information and tips for
troubleshooting, please
check the GROMACS
website at
http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb
file as well?
What are you choosing as your termini when running
pdb2gmx? It
should be "none," since by capping, you are
not choosing a
protonation state for the N- and C-termini.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au> <mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>>
<mailto:mark.abraham at anu.edu.au
<mailto:mark.abraham at anu.edu.au>
<mailto:mark.abraham at anu.edu.au
----- Original Message -----
From: Sai Pooja
<saipooja at gmail.com <mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>> <mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>
<mailto:saipooja at gmail.com
<mailto:saipooja at gmail.com>>>>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu
<mailto:jalemkul at vt.edu>
<mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
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Post by Sai Pooja
I am sorry if I did not frame the

question
correctly,
but putting
it very simply, is there a way to use
capping residues
with the
charmm forcefield if the residues are
--COCH3 and
NHCH3?
Yes - you edit a copy of the .rtp file
in your working
directory and
add whatever you want. Here's what I
use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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