[gmx-users] mktop

[ram bio]

Dear Gromacs Users,

I am using opls FF for my protein-ligand simulations in lipid bilayer. I
have generated the topologies for the ligand using MKtop. The output from
the MKTOP gives the top file, but not the coordinate/structure file. Please
let me know if any tutorial is available for merging the output of mktop
into gromacs MD simulation.



Thanks,

Pramod
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[Justin A. Lemkul]

Post by ram bio
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid bilayer. I
have generated the topologies for the ligand using MKtop. The output
from the MKTOP gives the top file, but not the coordinate/structure
file. Please let me know if any tutorial is available for merging the
output of mktop into gromacs MD simulation.

You can #include any molecule topology in a system .top, provided you have the
right format:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

There is no tutorial for using mktop with a protein-ligand/membrane system, but
there are tutorials for protein-ligand complexes:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

and membrane protein systems:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

-Justin
--
========================================

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

========================================

[ram bio]

Dear Justin,

Thanks for the information.

Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp; and
included the ligand.itp line in the topol.top file generated from the
pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of
ligand used as input for mktop were added to the output of pdb2gmx
(process.pdb - only protein coordinates), so that the structure file along
with ligand coordinates (processlig.pdb) can be used for further steps. I
doubt whether the procedure followed by me is correct, as when i execute
grompp command to add ions i am getting errors :


grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr


ERROR 1 [file ligand.itp, line 291]:
No default Ryckaert-Bell. types

..........

-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526

Fatal error:
[ file ligand.itp, line 397 ]:
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

The commands executed to reach the grompp step are as follows:


pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr

I have attached the topol.top, ligand.itp files for your information,
Please let me know your suggestions to fix this error.

Thanks,
Pramod

Post by Justin A. Lemkul

Post by ram bio
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid bilayer. I
have generated the topologies for the ligand using MKtop. The output from
the MKTOP gives the top file, but not the coordinate/structure file. Please
let me know if any tutorial is available for merging the output of mktop
into gromacs MD simulation.

You can #include any molecule topology in a system .top, provided you have
http://www.gromacs.org/**Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>
There is no tutorial for using mktop with a protein-ligand/membrane system,
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/membrane_**protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
-Justin
--
==============================**==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**==========
--
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[Justin A. Lemkul]

Post by ram bio
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp;
and included the ligand.itp line in the topol.top file generated from
the pdb2gmx. During the pdb2gmx command, i used opls FF. The
coordinates of ligand used as input for mktop were added to the output
of pdb2gmx (process.pdb - only protein coordinates), so that the
structure file along with ligand coordinates (processlig.pdb) can be
used for further steps. I doubt whether the procedure followed by me is
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
No default Ryckaert-Bell. types
..........
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
I have attached the topol.top, ligand.itp and procentsolv.gro files for
your information, Please let me know your suggestions to fix this error.

The ligand.itp file is trash. Most of your atoms have zero charge (except for a
few that have +/- 1...yikes!) and on line 397 (as cited in the error message)
atom 0 is referenced, which of course does not exist, since numbering starts
with 1. You also have some exotic atom types present, and thus bonded
parameters cannot be assigned, as grompp complained earlier.

You need a better quality topology, and perhaps a different force field that
might be suited for doing these simulations.

-Justin

Post by ram bio
Thanks,
Pramod
On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul <jalemkul at vt.edu
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid
bilayer. I have generated the topologies for the ligand using
MKtop. The output from the MKTOP gives the top file, but not the
coordinate/structure file. Please let me know if any tutorial is
available for merging the output of mktop into gromacs MD
simulation.
You can #include any molecule topology in a system .top, provided
http://www.gromacs.org/__Documentation/File_Formats/.__itp_File
<http://www.gromacs.org/Documentation/File_Formats/.itp_File>
There is no tutorial for using mktop with a protein-ligand/membrane
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
-Justin
--
==============================__==========
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> | [phone]
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
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<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
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<http://www.gromacs.org/Support/Mailing_Lists>

--
========================================

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

========================================

[ram bio]

Dear Justin,

As i generated the protein-ligand docked complex using opls FF, for the
consistency, i am trying to use opls ff generated ligand parameters during
md simulations in lipid bi layer. I found that MKTOP can generate topology
files using opls ff for small molecules.

I have also tried swiss param to generate the ligand parameters to be used
in protein ligand simulation using gromacs. The force field i am using for
simulations is OPLS. My ligand contains an azido group and a tropane ring
with protonated nitrogen. SwissParam force field has been designed to be
compatible with the Charmm force field, but they are not tested on
opls.Using the ligand topologies from swissparam, i was able to run the MD
simulations using gromacs with opls without errors (swissparam - gromacs
tutorial), only issues being the charges on the ligand, so i generated
various input files (mol2 files) for swissparam with charges generated
using ambcc1, gastergier and MMFF. But the itp files obtained from
swissparam had same charges for the ligand atoms irrespective of the input
provided i.e. charged or uncharged mol2 files, and

As per Gromacs website:

"Note that an .itp
file<http://www.gromacs.org/Documentation/File_Formats/.itp_File>will
be specific to a given force field, and will only function when
included by a .top
file<http://www.gromacs.org/Documentation/File_Formats/.top_File>that
has previously included the .itp
files <http://www.gromacs.org/Documentation/File_Formats/.itp_File> for that
force field. Appropriate use of the #define and #ifdef mechanisms can permit
the same .itp file<http://www.gromacs.org/Documentation/File_Formats/.itp_File>to
work with multiple force fields, e.g.
share/top/water.itp."

so, i think even though the swissparam generated topologies based on MMFF
fit to charmm (based on testing), they could also be used with opls. It was
informed by swiss param team that the ligand parameters generated by
swissparam could also be used with opls FF in principle as they are based on
MMFF
So, in order to cross check or validate my results i was trying to use mktop
to generate the ligand topologies for MD simulations.

Please let me know your comments and suggestions on the procedure ,
regarding the compatibility of MMFF generated topologies to be used by OPLS
and other methods to validate my results.

Thanks,

Pramod

Post by Justin A. Lemkul

Post by ram bio
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp; and
included the ligand.itp line in the topol.top file generated from the
pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of
ligand used as input for mktop were added to the output of pdb2gmx
(process.pdb - only protein coordinates), so that the structure file along
with ligand coordinates (processlig.pdb) can be used for further steps. I
doubt whether the procedure followed by me is correct, as when i execute
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
No default Ryckaert-Bell. types
..........
------------------------------**-------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
------------------------------**-------------------------
pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
I have attached the topol.top, ligand.itp and procentsolv.gro files for
your information, Please let me know your suggestions to fix this error.

The ligand.itp file is trash. Most of your atoms have zero charge (except
for a few that have +/- 1...yikes!) and on line 397 (as cited in the error
message) atom 0 is referenced, which of course does not exist, since
numbering starts with 1. You also have some exotic atom types present, and
thus bonded parameters cannot be assigned, as grompp complained earlier.
You need a better quality topology, and perhaps a different force field
that might be suited for doing these simulations.
-Justin
Thanks,

Post by ram bio
Pramod
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid
bilayer. I have generated the topologies for the ligand using
MKtop. The output from the MKTOP gives the top file, but not the
coordinate/structure file. Please let me know if any tutorial is
available for merging the output of mktop into gromacs MD
simulation.
You can #include any molecule topology in a system .top, provided
http://www.gromacs.org/__**Documentation/File_Formats/.__**itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File>
<http://www.gromacs.org/**Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>
There is no tutorial for using mktop with a protein-ligand/membrane
http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin/_**
_gmx-tutorials/complex/index._**_html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html>
<http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin/_**
_gmx-tutorials/membrane___**protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html>
<http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/membrane_**protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
-Justin
-- ==============================**__==========
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> | [phone]
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**__==========
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.

Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

--
==============================**==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

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[Justin A. Lemkul]

Post by ram bio
Dear Justin,
As i generated the protein-ligand docked complex using opls FF, for the
consistency, i am trying to use opls ff generated ligand parameters
during md simulations in lipid bi layer. I found that MKTOP can generate
topology files using opls ff for small molecules.

I understand that. The program did a poor job, per the reasons I cited before.
I do not know anything about mktop (other than what it does), so I cannot
analyze its suitability here, but due to missing parameters and bogus charges,
you should not use that topology for anything.

Post by ram bio
I have also tried swiss param to generate the ligand parameters to be
used in protein ligand simulation using gromacs. The force field i am
using for simulations is OPLS. My ligand contains an azido group and a
tropane ring with protonated nitrogen. SwissParam force field has been
designed to be compatible with the Charmm force field, but they are not
tested on opls.Using the ligand topologies from swissparam, i was able
to run the MD simulations using gromacs with opls without errors
(swissparam - gromacs tutorial), only issues being the charges on the
ligand, so i generated various input files (mol2 files) for swissparam
with charges generated using ambcc1, gastergier and MMFF. But the itp
files obtained from swissparam had same charges for the ligand atoms
irrespective of the input provided i.e. charged or uncharged mol2 files, and

If SwissParam was designed to be used with CHARMM, the most intuitive next step
is to use CHARMM for the MD, is it not? I understand the point about trying to
keep the force fields consistent between docking and MD, but it may not be
feasible (i.e., there may not be suitable parameters in OPLS for the bizarre
functional groups you're dealing with).

Post by ram bio
"Note that an .itp file
<http://www.gromacs.org/Documentation/File_Formats/.itp_File> will be
specific to a given force field, and will only function when included by
a .top file
<http://www.gromacs.org/Documentation/File_Formats/.top_File> that has
previously included the .itp files
<http://www.gromacs.org/Documentation/File_Formats/.itp_File> for that
force field. Appropriate use of the |#define| and |#ifdef| mechanisms
can permit the same .itp file
<http://www.gromacs.org/Documentation/File_Formats/.itp_File> to work
with multiple force fields, e.g. |share/top/water.itp|."

Note the key caveat here - through the use of #define and #ifdef you can make
use of different force fields. That means you can control which parameters are
applied based on different conditions. I could write an .itp file for any
molecule that has force field parameters for any force field, and all I'd have
to do is enclose all relevant directives within #ifdef blocks and it would work.
This note does *not* indicate that you can mix and match force fields. Doing
so is generally a very bad idea, if it even works syntactically.

Post by ram bio
so, i think even though the swissparam generated topologies based on
MMFF fit to charmm (based on testing), they could also be used with
opls. It was informed by swiss param team that the ligand parameters
generated by swissparam could also be used with opls FF in principle as
they are based on MMFF
So, in order to cross check or validate my results i was trying to use
mktop to generate the ligand topologies for MD simulations.

Maybe the SwissParam-generated topology will work. There are commonalities
underlying these force fields, to be sure. Still, the methodology for properly
deriving OPLS parameters is quite well described in the literature, right down
to the QM basis sets required to run the geometry optimizations and charge
calculations.

-Justin

Post by ram bio
Please let me know your comments and suggestions on the procedure ,
regarding the compatibility of MMFF generated topologies to be used by
OPLS and other methods to validate my results.
Thanks,
Pramod
On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul <jalemkul at vt.edu
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand
in water solvent . I renamed the topology.top generated from
mktop to ligand.itp; and included the ligand.itp line in the
topol.top file generated from the pdb2gmx. During the pdb2gmx
command, i used opls FF. The coordinates of ligand used as
input for mktop were added to the output of pdb2gmx (process.pdb
- only protein coordinates), so that the structure file along
with ligand coordinates (processlig.pdb) can be used for further
steps. I doubt whether the procedure followed by me is correct,
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
No default Ryckaert-Bell. types
..........
------------------------------__-------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/__Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>
------------------------------__-------------------------
pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
I have attached the topol.top, ligand.itp and procentsolv.gro
files for your information, Please let me know your suggestions
to fix this error.
The ligand.itp file is trash. Most of your atoms have zero charge
(except for a few that have +/- 1...yikes!) and on line 397 (as
cited in the error message) atom 0 is referenced, which of course
does not exist, since numbering starts with 1. You also have some
exotic atom types present, and thus bonded parameters cannot be
assigned, as grompp complained earlier.
You need a better quality topology, and perhaps a different force
field that might be suited for doing these simulations.
-Justin
Thanks,
Pramod
On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid
bilayer. I have generated the topologies for the ligand using
MKtop. The output from the MKTOP gives the top file, but not the
coordinate/structure file. Please let me know if any tutorial is
available for merging the output of mktop into gromacs MD
simulation.
You can #include any molecule topology in a system .top, provided
http://www.gromacs.org/____Documentation/File_Formats/.____itp_File
<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File>
<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File
<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
There is no tutorial for using mktop with a
protein-ligand/membrane
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin/____gmx-tutorials/complex/index.____html
<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>>
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin/____gmx-tutorials/membrane_____protein/index.html
<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>>
-Justin
-- ==============================____==========
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 <tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
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--
==============================__==========
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> | [phone]
<tel:%28540%29%20231-9080>
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--
========================================

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

========================================

[ram bio]

Dear Justin,

Thanks, and I accept your suggestions;

If SwissParam was designed to be used with CHARMM, the most intuitive next
step is to use CHARMM for the MD, is it not?I understand the point about
trying to keep the force fields consistent between docking and MD, but it
may not be feasible (i.e., there may not be suitable parameters in OPLS for
the bizarre functional groups you're dealing with).

Yes, I also tried CHARMM FF to generate the topology file of the protein
using pdb2gmx (without ligand), and as per the swissparam and gromacs
tutorial i could build the protein-ligand-lipid bilayer and minimize it
using mdrun and and i am at the NPT equilibration step, everything is ok
with this procedure and without errors, but my lipid bilayer is made up of
POPC and the POPC itp file has OPLS FF topologies. So, i was wondering
whether the POPC itp file i am using for MD simulations can be used with the
protein and ligand topology file generated by CHARMM.

and as per the swissparam tutorial the command to generate topology file for
protein is:

pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp



in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx
command is available, but i could not understand the usage of -nochargegp
flag as per the tutorial, is this flag still valid while generating
toplogies.

Please let me know your comments and suggestions regarding the procedure
followed and the itp files usage for gromacs MD simulations.

Thanks in advance,

Pramod

Post by Justin A. Lemkul

Post by ram bio
Dear Justin,
As i generated the protein-ligand docked complex using opls FF, for the
consistency, i am trying to use opls ff generated ligand parameters during
md simulations in lipid bi layer. I found that MKTOP can generate topology
files using opls ff for small molecules.

I understand that. The program did a poor job, per the reasons I cited
before. I do not know anything about mktop (other than what it does), so I
cannot analyze its suitability here, but due to missing parameters and bogus
charges, you should not use that topology for anything.
I have also tried swiss param to generate the ligand parameters to be

Post by ram bio
used in protein ligand simulation using gromacs. The force field i am using
for simulations is OPLS. My ligand contains an azido group and a tropane
ring with protonated nitrogen. SwissParam force field has been designed to
be compatible with the Charmm force field, but they are not tested on
opls.Using the ligand topologies from swissparam, i was able to run the MD
simulations using gromacs with opls without errors (swissparam - gromacs
tutorial), only issues being the charges on the ligand, so i generated
various input files (mol2 files) for swissparam with charges generated
using ambcc1, gastergier and MMFF. But the itp files obtained from
swissparam had same charges for the ligand atoms irrespective of the input
provided i.e. charged or uncharged mol2 files, and

If SwissParam was designed to be used with CHARMM, the most intuitive next
step is to use CHARMM for the MD, is it not? I understand the point about
trying to keep the force fields consistent between docking and MD, but it
may not be feasible (i.e., there may not be suitable parameters in OPLS for
the bizarre functional groups you're dealing with).

Post by ram bio
"Note that an .itp file <http://www.gromacs.org/**
Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
will be specific to a given force field, and will only function when
included by a .top file <http://www.gromacs.org/**
Documentation/File_Formats/.**top_File<http://www.gromacs.org/Documentation/File_Formats/.top_File>>
that has previously included the .itp files <http://www.gromacs.org/**
Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
for that force field. Appropriate use of the |#define| and |#ifdef|
mechanisms can permit the same .itp file <http://www.gromacs.org/**
Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
to work with multiple force fields, e.g. |share/top/water.itp|."

Note the key caveat here - through the use of #define and #ifdef you can
make use of different force fields. That means you can control which
parameters are applied based on different conditions. I could write an .itp
file for any molecule that has force field parameters for any force field,
and all I'd have to do is enclose all relevant directives within #ifdef
blocks and it would work. This note does *not* indicate that you can mix
and match force fields. Doing so is generally a very bad idea, if it even
works syntactically.
so, i think even though the swissparam generated topologies based on MMFF

Post by ram bio
fit to charmm (based on testing), they could also be used with opls. It was
informed by swiss param team that the ligand parameters generated by
swissparam could also be used with opls FF in principle as they are based on
MMFF
So, in order to cross check or validate my results i was trying to use
mktop to generate the ligand topologies for MD simulations.

Maybe the SwissParam-generated topology will work. There are commonalities
underlying these force fields, to be sure. Still, the methodology for
properly deriving OPLS parameters is quite well described in the literature,
right down to the QM basis sets required to run the geometry optimizations
and charge calculations.
-Justin
Please let me know your comments and suggestions on the procedure ,

Post by ram bio
regarding the compatibility of MMFF generated topologies to be used by OPLS
and other methods to validate my results.
Thanks,
Pramod
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand
in water solvent . I renamed the topology.top generated from
mktop to ligand.itp; and included the ligand.itp line in the
topol.top file generated from the pdb2gmx. During the pdb2gmx
command, i used opls FF. The coordinates of ligand used as
input for mktop were added to the output of pdb2gmx (process.pdb
- only protein coordinates), so that the structure file along
with ligand coordinates (processlig.pdb) can be used for further
steps. I doubt whether the procedure followed by me is correct,
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
No default Ryckaert-Bell. types
..........
------------------------------**__-------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors>
<http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
------------------------------**__-------------------------
pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
I have attached the topol.top, ligand.itp and procentsolv.gro
files for your information, Please let me know your suggestions
to fix this error.
The ligand.itp file is trash. Most of your atoms have zero charge
(except for a few that have +/- 1...yikes!) and on line 397 (as
cited in the error message) atom 0 is referenced, which of course
does not exist, since numbering starts with 1. You also have some
exotic atom types present, and thus bonded parameters cannot be
assigned, as grompp complained earlier.
You need a better quality topology, and perhaps a different force
field that might be suited for doing these simulations.
-Justin
Thanks,
Pramod
On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul
<jalemkul at vt.edu <mailto:jalemkul at vt.edu>
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid
bilayer. I have generated the topologies for the ligand using
MKtop. The output from the MKTOP gives the top file, but not the
coordinate/structure file. Please let me know if any tutorial is
available for merging the output of mktop into gromacs MD
simulation.
You can #include any molecule topology in a system .top, provided
http://www.gromacs.org/____**
Documentation/File_Formats/.__**__itp_File<http://www.gromacs.org/____Documentation/File_Formats/.____itp_File>
<http://www.gromacs.org/__**Documentation/File_Formats/.__**
itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File>
<http://www.gromacs.org/__**
Documentation/File_Formats/.__**itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File>
<http://www.gromacs.org/**Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>
There is no tutorial for using mktop with a
protein-ligand/membrane
http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/
**justin/____gmx-tutorials/**complex/index.____html<http://vt.edu/Pages/Personal/justin/____gmx-tutorials/complex/index.____html>
<http://vt.edu/Pages/Personal/**justin/__gmx-tutorials/**
complex/index.__html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html>
<http://www.bevanlab.biochem._**_
vt.edu/Pages/Personal/justin/**__gmx-tutorials/complex/index.**__html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html>
<http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/
**justin/____gmx-tutorials/**membrane_____protein/index.**html<http://vt.edu/Pages/Personal/justin/____gmx-tutorials/membrane_____protein/index.html>
<http://vt.edu/Pages/Personal/**justin/__gmx-tutorials/**
membrane___protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html>
<http://www.bevanlab.biochem._**_
vt.edu/Pages/Personal/justin/**__gmx-tutorials/membrane___**
protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html>
<http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/membrane_**protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
-Justin
-- ==============================**____==========
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 <tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**____==========
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-- ==============================**__==========
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> | [phone]
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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--
==============================**==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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[Justin A. Lemkul]

Post by ram bio
Dear Justin,
Thanks, and I accept your suggestions;
If SwissParam was designed to be used with CHARMM, the most intuitive
next step is to use CHARMM for the MD, is it not?I understand the point
about trying to keep the force fields consistent between docking and MD,
but it may not be feasible (i.e., there may not be suitable parameters
in OPLS for the bizarre functional groups you're dealing with).
Yes, I also tried CHARMM FF to generate the topology file of the protein
using pdb2gmx (without ligand), and as per the swissparam and gromacs
tutorial i could build the protein-ligand-lipid bilayer and minimize it
using mdrun and and i am at the NPT equilibration step, everything is ok
with this procedure and without errors, but my lipid bilayer is made up
of POPC and the POPC itp file has OPLS FF topologies. So, i was
wondering whether the POPC itp file i am using for MD simulations can be
used with the protein and ligand topology file generated by CHARMM.

You shouldn't mix and match force fields. Suitable CHARMM lipid parameters are
widely available.

Post by ram bio
and as per the swissparam tutorial the command to generate topology file
pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp
in the gromacs 4.5.4 version the option to select Charmm FF from the
pdb2gmx command is available, but i could not understand the usage of
-nochargegp flag as per the tutorial, is this flag still valid while
generating toplogies.

CHARMM does not use charge groups. Therefore, each atom should be its own
"group" in the topology. Using -nochargegrp overrides the default behavior of
the .rtp files (which has multi-atom charge groups, although I think this was
changed somewhere along the way, but I don't remember if it was before or after
4.5.4).

-Justin
--
========================================

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

========================================

[ram bio]

Dear Justin,


Thanks.

The POPC bilayer i am using is with berger lipids, corrected for dihedrals
so as to be compatible with the OPLS FF for aminoacids.

While searching for the literature on compatibility of lipid FF and protein
FF, I found few references where similar modification was done for DOPC
lipid bilayer and were suitable with various FF for proteins and also with
CHARMM FF:

1. Membrane protein simulations with a united-atom lipid and all-atom
protein model: lipid?protein interactions, side chain transfer free energies
and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221?S1234

2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force
Fields.J Comput Chem 32: 1400?1410, 2011.

I don't have the lipid bilayer with their itp files with CHARMM FF
parameterization. Please could you inform me where to obtain them, so that i
can use the lipid bilayer structure for embedding the protein and use the
related CHARMM FF parameterised itp in the topology file in gromacs for MD
simulation.

Thanks in advance,

Pramod

Post by Justin A. Lemkul

Post by ram bio
Dear Justin,
Thanks, and I accept your suggestions;
If SwissParam was designed to be used with CHARMM, the most intuitive next
step is to use CHARMM for the MD, is it not?I understand the point about
trying to keep the force fields consistent between docking and MD, but it
may not be feasible (i.e., there may not be suitable parameters in OPLS for
the bizarre functional groups you're dealing with).
Yes, I also tried CHARMM FF to generate the topology file of the protein
using pdb2gmx (without ligand), and as per the swissparam and gromacs
tutorial i could build the protein-ligand-lipid bilayer and minimize it
using mdrun and and i am at the NPT equilibration step, everything is ok
with this procedure and without errors, but my lipid bilayer is made up of
POPC and the POPC itp file has OPLS FF topologies. So, i was wondering
whether the POPC itp file i am using for MD simulations can be used with the
protein and ligand topology file generated by CHARMM.

You shouldn't mix and match force fields. Suitable CHARMM lipid parameters
are widely available.
and as per the swissparam tutorial the command to generate topology file

Post by ram bio
pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp
in the gromacs 4.5.4 version the option to select Charmm FF from the
pdb2gmx command is available, but i could not understand the usage of
-nochargegp flag as per the tutorial, is this flag still valid while
generating toplogies.

CHARMM does not use charge groups. Therefore, each atom should be its own
"group" in the topology. Using -nochargegrp overrides the default behavior
of the .rtp files (which has multi-atom charge groups, although I think this
was changed somewhere along the way, but I don't remember if it was before
or after 4.5.4).
-Justin
--
==============================**==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**==========
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[Justin A. Lemkul]

Post by ram bio
Dear Justin,
Thanks.
The POPC bilayer i am using is with berger lipids, corrected for
dihedrals so as to be compatible with the OPLS FF for aminoacids.

I think significantly more parameters than just dihedrals need to be altered to
make the Berger united-atom force field compatible with OPLS.

Post by ram bio
While searching for the literature on compatibility of lipid FF and
protein FF, I found few references where similar modification was done
for DOPC lipid bilayer and were suitable with various FF for proteins
1. Membrane protein simulations with a united-atom lipid and all-atom
protein model: lipid?protein interactions, side chain transfer free
energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221?S1234
2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force
Fields.J Comput Chem 32: 1400?1410, 2011.
I don't have the lipid bilayer with their itp files with CHARMM FF
parameterization. Please could you inform me where to obtain them, so
that i can use the lipid bilayer structure for embedding the protein and
use the related CHARMM FF parameterised itp in the topology file in
gromacs for MD simulation.

The lipids are built into the CHARMM27 implementation in Gromacs. You can
generate their topology with pdb2gmx. Run pdb2gmx on a single lipid, convert it
to an .itp file, and #include it in the topology. The CHARMM36 force field is
also available in the User Contributions section of the Gromacs website.

-Justin

Post by ram bio
Thanks in advance,
Pramod
On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul <jalemkul at vt.edu
Dear Justin,
Thanks, and I accept your suggestions;
If SwissParam was designed to be used with CHARMM, the most
intuitive next step is to use CHARMM for the MD, is it not?I
understand the point about trying to keep the force fields
consistent between docking and MD, but it may not be feasible
(i.e., there may not be suitable parameters in OPLS for the
bizarre functional groups you're dealing with).
Yes, I also tried CHARMM FF to generate the topology file of the
protein using pdb2gmx (without ligand), and as per the
swissparam and gromacs tutorial i could build the
protein-ligand-lipid bilayer and minimize it using mdrun and and
i am at the NPT equilibration step, everything is ok with this
procedure and without errors, but my lipid bilayer is made up of
POPC and the POPC itp file has OPLS FF topologies. So, i was
wondering whether the POPC itp file i am using for MD
simulations can be used with the protein and ligand topology
file generated by CHARMM.
You shouldn't mix and match force fields. Suitable CHARMM lipid
parameters are widely available.
and as per the swissparam tutorial the command to generate
pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o
conf.pdb -nochargegrp
in the gromacs 4.5.4 version the option to select Charmm FF from
the pdb2gmx command is available, but i could not understand the
usage of -nochargegp flag as per the tutorial, is this flag
still valid while generating toplogies.
CHARMM does not use charge groups. Therefore, each atom should be
its own "group" in the topology. Using -nochargegrp overrides the
default behavior of the .rtp files (which has multi-atom charge
groups, although I think this was changed somewhere along the way,
but I don't remember if it was before or after 4.5.4).
-Justin
--
==============================__==========
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> | [phone]
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
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<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www
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Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>

--
========================================

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

========================================