Discussion:
pdb2gmx problems and modified AA's
(too old to reply)
Dr Seth Carlton OLSEN
2004-10-09 08:05:06 UTC
Permalink
Hi Gromacs Users,

I am trying to run a pdb through pdb2gmx to get files to do an md run. The protein chain contains an unconventional residue ('CRQ', in the pdb). I am using the OPLS-AA forcefield. I have modified the ffoplsaa.rtp, ffoplsaa.hdb and aminoacids.dat files by adding the following sections:
**added to ffoplsaa.rtp
;CRQ - chromophore GYQ from Rtms5 structure
[CRQ]
[ atoms ]
CD1 opls_145 0.029 1
HD11 opls_146 0.000 1
CE1 opls_145 0.030 1
HE11 opls_146 0.000 1
CZ opls_166 0.204 1
OH opls_167 -1.316 1
CE2 opls_145 0.029 1
HE21 opls_146 0.000 1
CD2 opls_145 0.029 1
HD21 opls_146 0.000 1
CG2 opls_145 0.050 1
CB2 opls_142 0.064 1
HB21 opls_144 0.000 1
CA2 opls_141 0.204 1
N2 opls_559 -0.436 1
C2 opls_235 0.340 1
O2 opls_236 -0.632 1
N3 opls_557 0.110 1
CA3 opls_223 0.134 1
HA31 opls_140 0.000 1
HA32 opls_140 0.000 1
C opls_235 0.433 1
O opls_236 -1.316 1
C1 opls_558 0.340 1
CA1 opls_257 0.204 1
N opls_251 -0.838 1
CB1 opls_136 0.133 1
HB11 opls_140 0.000 1
HB12 opls_140 0.000 1
CG1 opls_136 0.133 1
HG11 opls_140 0.000 1
HG12 opls_140 0.000 1
CD3 opls_139 0.433 1
OE1 opls_235 -0.632 1
NE1 opls_237 0.127 1
HAE opls_909 0.072 1
HAD opls_909 0.072 1
[ bonds ]
CD1 CE1
CD1 HD11
CD1 CG2
CE1 CZ
CE1 HE11
CZ OH
CZ CE2
CE2 CD2
CE2 HE21
CD2 CG2
CD2 HD21
CG2 CB2
CB2 CA2
CB2 HB21
CA2 N2
CA2 C2
N2 C1
C2 O2
C2 N3
N3 CA3
N3 C1
CA3 C
CA3 HA31
CA3 HA32
C O
C1 CA1
CA1 N
CA1 CB1
CB1 CG1
CB1 HB11
CB1 HB12
CG1 CD3
CG1 HG11
CG1 HG12
CD3 OE1
CD3 NE1
NE1 HAE
NE1 HAD
-C N
[ impropers ]
CA +N C O improper_O_C_X_Y

***added to ffoplsaa.hdb
CRQ 9
1 1 CD1 CE1 CG2
1 1 CE1 OH CD1
1 1 CD2 CE2 CG2
1 1 CE2 OH CD2
1 1 CB2 CG2 CA2
2 6 CB1 CA1 CG1
2 6 CG1 CB1 CD3
2 3 NE1 CD3 OE1
2 6 CA3 N3 C

***added to aminoacids.dat
CRQ


when I run pdb2gmx on the pdb file 'pdb1mou.ent' (too large to be included here) I get the following error, which kills pdb2gmx:
Fatal error: Atom HE12 not found in rtp database in residue CRQ, it looks a bit like HE11

However, I am not sure why pdb2gmx is looking for this atom. HE12 is not included in the pdb file (which, as expected, does not contain hydrogens). Why is pdb2gmx looking for an atom that does not exist and should not? Is there a naming convention in operation of which I am not aware? Is pdb2gmx anticipating the naming of the hydrogens to be put in the structure?

If anyone has any insight into this problem, I would be very grateful. For the moment, it has stopped me in my tracks.

Cheers,

Seth



ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
David
2004-10-09 08:37:35 UTC
Permalink
Post by Dr Seth Carlton OLSEN
Hi Gromacs Users,
**added to ffoplsaa.rtp
;CRQ - chromophore GYQ from Rtms5 structure
[CRQ]
[ atoms ]
CD1 opls_145 0.029 1
HD11 opls_146 0.000 1
CE1 opls_145 0.030 1
HE11 opls_146 0.000 1
CZ opls_166 0.204 1
OH opls_167 -1.316 1
CE2 opls_145 0.029 1
HE21 opls_146 0.000 1
CD2 opls_145 0.029 1
HD21 opls_146 0.000 1
CG2 opls_145 0.050 1
CB2 opls_142 0.064 1
HB21 opls_144 0.000 1
CA2 opls_141 0.204 1
N2 opls_559 -0.436 1
C2 opls_235 0.340 1
O2 opls_236 -0.632 1
N3 opls_557 0.110 1
CA3 opls_223 0.134 1
HA31 opls_140 0.000 1
HA32 opls_140 0.000 1
C opls_235 0.433 1
O opls_236 -1.316 1
C1 opls_558 0.340 1
CA1 opls_257 0.204 1
N opls_251 -0.838 1
CB1 opls_136 0.133 1
HB11 opls_140 0.000 1
HB12 opls_140 0.000 1
CG1 opls_136 0.133 1
HG11 opls_140 0.000 1
HG12 opls_140 0.000 1
CD3 opls_139 0.433 1
OE1 opls_235 -0.632 1
NE1 opls_237 0.127 1
HAE opls_909 0.072 1
HAD opls_909 0.072 1
[ bonds ]
CD1 CE1
CD1 HD11
CD1 CG2
CE1 CZ
CE1 HE11
CZ OH
CZ CE2
CE2 CD2
CE2 HE21
CD2 CG2
CD2 HD21
CG2 CB2
CB2 CA2
CB2 HB21
CA2 N2
CA2 C2
N2 C1
C2 O2
C2 N3
N3 CA3
N3 C1
CA3 C
CA3 HA31
CA3 HA32
C O
C1 CA1
CA1 N
CA1 CB1
CB1 CG1
CB1 HB11
CB1 HB12
CG1 CD3
CG1 HG11
CG1 HG12
CD3 OE1
CD3 NE1
NE1 HAE
NE1 HAD
-C N
[ impropers ]
CA +N C O improper_O_C_X_Y
***added to ffoplsaa.hdb
CRQ 9
1 1 CD1 CE1 CG2
1 1 CE1 OH CD1
1 1 CD2 CE2 CG2
1 1 CE2 OH CD2
1 1 CB2 CG2 CA2
2 6 CB1 CA1 CG1
2 6 CG1 CB1 CD3
2 3 NE1 CD3 OE1
2 6 CA3 N3 C
***added to aminoacids.dat
CRQ
Fatal error: Atom HE12 not found in rtp database in residue CRQ, it looks a bit like HE11
pdb2gmx makes hydrogens by modifying the name of the atom it is bound
to. In your case you have NE1, so it wants to make HE12 and HE11. You
have however also a CE1. I would recommend to rename NE1 to NE2 and the
hydrogens to HE21 and HE22.

Did you also modify the ffoplsaa.hdb file?
Post by Dr Seth Carlton OLSEN
However, I am not sure why pdb2gmx is looking for this atom. HE12 is not included in the pdb file (which, as expected, does not contain hydrogens). Why is pdb2gmx looking for an atom that does not exist and should not? Is there a naming convention in operation of which I am not aware? Is pdb2gmx anticipating the naming of the hydrogens to be put in the structure?
If anyone has any insight into this problem, I would be very grateful. For the moment, it has stopped me in my tracks.
Cheers,
Seth
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr Seth Carlton OLSEN
2004-10-09 09:29:18 UTC
Permalink
Hi Gromacs Users,

Regarding the warning below that atom 'O2' is missing from the pdb, does this relate to the fact that atom 'O' was removed during the workings of pdb2gmx? If 'O' was removed (the program said it was redundant) and 'O2' was named 'O' this would be consistent with the warning. Is this what's happening? Why does pdb2gmx not want to take the name 'O2', and why does it appear to rename the atom in conflict with another and then delete one of the pair it then believes is redundant?

Cheers,

Seth



Hi Gromacs Users,

Thanks David for that point. I have renamed NE1 to NE3 (since there is also a CE2) in the rtp, hdb files and in the pdb I'm trying to process. The fatal error then read:

Fatal error: Atom HE31 not found in rtp database in residue CRQ, it looks a bit like HE11

Accordingly, I changed the nitrogen-bonded hydrogen atoms (there should be 2) to HE31 and HE32 respectively. However, this generated the following fatal errors:

WARNING: atom HD11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HE11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HE11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HE21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HE21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HD21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HB21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HB21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom O2 is missing in residue CRQ 62 in the pdb file

Fatal error: There were 6 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing

I have added the requisite lines to the hbd file, so I'm not sure why it does not find them. The hydrogens are not in the pdb file - I am adding them through the use of pdb2gmx. I'm not sure why it states that 02 is not in the pdb, since it is definitely there. Does pdb2gmx expect to find the hydrogens in the pdb file?

Cheers,

Seth

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms




----- Original Message -----
From: David <spoel at xray.bmc.uu.se>
Date: Saturday, October 9, 2004 6:37 pm
Subject: Re: [gmx-users] pdb2gmx problems and modified AA's
Post by Dr Seth Carlton OLSEN
Post by Dr Seth Carlton OLSEN
Hi Gromacs Users,
I am trying to run a pdb through pdb2gmx to get files to do an md
run. The protein chain contains an unconventional residue ('CRQ',
in the pdb). I am using the OPLS-AA forcefield. I have modified
the ffoplsaa.rtp, ffoplsaa.hdb and aminoacids.dat files by adding
Post by Dr Seth Carlton OLSEN
**added to ffoplsaa.rtp
;CRQ - chromophore GYQ from Rtms5 structure
[CRQ]
[ atoms ]
CD1 opls_145 0.029 1
HD11 opls_146 0.000 1
CE1 opls_145 0.030 1
HE11 opls_146 0.000 1
CZ opls_166 0.204 1
OH opls_167 -1.316 1
CE2 opls_145 0.029 1
HE21 opls_146 0.000 1
CD2 opls_145 0.029 1
HD21 opls_146 0.000 1
CG2 opls_145 0.050 1
CB2 opls_142 0.064 1
HB21 opls_144 0.000 1
CA2 opls_141 0.204 1
N2 opls_559 -0.436 1
C2 opls_235 0.340 1
O2 opls_236 -0.632 1
N3 opls_557 0.110 1
CA3 opls_223 0.134 1
HA31 opls_140 0.000 1
HA32 opls_140 0.000 1
C opls_235 0.433 1
O opls_236 -1.316 1
C1 opls_558 0.340 1
CA1 opls_257 0.204 1
N opls_251 -0.838 1
CB1 opls_136 0.133 1
HB11 opls_140 0.000 1
HB12 opls_140 0.000 1
CG1 opls_136 0.133 1
HG11 opls_140 0.000 1
HG12 opls_140 0.000 1
CD3 opls_139 0.433 1
OE1 opls_235 -0.632 1
NE1 opls_237 0.127 1
HAE opls_909 0.072 1
HAD opls_909 0.072 1
[ bonds ]
CD1 CE1
CD1 HD11
CD1 CG2
CE1 CZ
CE1 HE11
CZ OH
CZ CE2
CE2 CD2
CE2 HE21
CD2 CG2
CD2 HD21
CG2 CB2
CB2 CA2
CB2 HB21
CA2 N2
CA2 C2
N2 C1
C2 O2
C2 N3
N3 CA3
N3 C1
CA3 C
CA3 HA31
CA3 HA32
C O
C1 CA1
CA1 N
CA1 CB1
CB1 CG1
CB1 HB11
CB1 HB12
CG1 CD3
CG1 HG11
CG1 HG12
CD3 OE1
CD3 NE1
NE1 HAE
NE1 HAD
-C N
[ impropers ]
CA +N C O improper_O_C_X_Y
***added to ffoplsaa.hdb
CRQ 9
1 1 CD1 CE1 CG2
1 1 CE1 OH CD1
1 1 CD2 CE2 CG2
1 1 CE2 OH CD2
1 1 CB2 CG2 CA2
2 6 CB1 CA1 CG1
2 6 CG1 CB1 CD3
2 3 NE1 CD3 OE1
2 6 CA3 N3 C
***added to aminoacids.dat
CRQ
when I run pdb2gmx on the pdb file 'pdb1mou.ent' (too large to be
Fatal error: Atom HE12 not found in rtp database in residue CRQ,
it looks a bit like HE11
pdb2gmx makes hydrogens by modifying the name of the atom it is bound
to. In your case you have NE1, so it wants to make HE12 and HE11. You
have however also a CE1. I would recommend to rename NE1 to NE2 and
thehydrogens to HE21 and HE22.
Did you also modify the ffoplsaa.hdb file?
Post by Dr Seth Carlton OLSEN
However, I am not sure why pdb2gmx is looking for this atom.
HE12 is not included in the pdb file (which, as expected, does not
contain hydrogens). Why is pdb2gmx looking for an atom that does
not exist and should not? Is there a naming convention in
operation of which I am not aware? Is pdb2gmx anticipating the
naming of the hydrogens to be put in the structure?
Post by Dr Seth Carlton OLSEN
If anyone has any insight into this problem, I would be very
grateful. For the moment, it has stopped me in my tracks.
Post by Dr Seth Carlton OLSEN
Cheers,
Seth
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
David
2004-10-09 10:05:46 UTC
Permalink
Post by Dr Seth Carlton OLSEN
Hi Gromacs Users,
Regarding the warning below that atom 'O2' is missing from the pdb, does this relate to the fact that atom 'O' was removed during the workings of pdb2gmx? If 'O' was removed (the program said it was redundant) and 'O2' was named 'O' this would be consistent with the warning. Is this what's happening? Why does pdb2gmx not want to take the name 'O2', and why does it appear to rename the atom in conflict with another and then delete one of the pair it then believes is redundant?
O2 is regarded as a C-terminal oxygen and is renamed to O. Your best bet
is renaming the O to something else.

As regards the HE31 etc. that should be possible to resolve by changing
atom names too.
Post by Dr Seth Carlton OLSEN
Cheers,
Seth
Hi Gromacs Users,
Fatal error: Atom HE31 not found in rtp database in residue CRQ, it looks a bit like HE11
WARNING: atom HD11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)
WARNING: atom HE11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HE11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)
WARNING: atom HE21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HE21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)
WARNING: atom HD21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)
WARNING: atom HB21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HB21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)
WARNING: atom O2 is missing in residue CRQ 62 in the pdb file
Fatal error: There were 6 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing
I have added the requisite lines to the hbd file, so I'm not sure why it does not find them. The hydrogens are not in the pdb file - I am adding them through the use of pdb2gmx. I'm not sure why it states that 02 is not in the pdb, since it is definitely there. Does pdb2gmx expect to find the hydrogens in the pdb file?
Cheers,
Seth
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
----- Original Message -----
From: David <spoel at xray.bmc.uu.se>
Date: Saturday, October 9, 2004 6:37 pm
Subject: Re: [gmx-users] pdb2gmx problems and modified AA's
Post by Dr Seth Carlton OLSEN
Post by Dr Seth Carlton OLSEN
Hi Gromacs Users,
I am trying to run a pdb through pdb2gmx to get files to do an md
run. The protein chain contains an unconventional residue ('CRQ',
in the pdb). I am using the OPLS-AA forcefield. I have modified
the ffoplsaa.rtp, ffoplsaa.hdb and aminoacids.dat files by adding
Post by Dr Seth Carlton OLSEN
**added to ffoplsaa.rtp
;CRQ - chromophore GYQ from Rtms5 structure
[CRQ]
[ atoms ]
CD1 opls_145 0.029 1
HD11 opls_146 0.000 1
CE1 opls_145 0.030 1
HE11 opls_146 0.000 1
CZ opls_166 0.204 1
OH opls_167 -1.316 1
CE2 opls_145 0.029 1
HE21 opls_146 0.000 1
CD2 opls_145 0.029 1
HD21 opls_146 0.000 1
CG2 opls_145 0.050 1
CB2 opls_142 0.064 1
HB21 opls_144 0.000 1
CA2 opls_141 0.204 1
N2 opls_559 -0.436 1
C2 opls_235 0.340 1
O2 opls_236 -0.632 1
N3 opls_557 0.110 1
CA3 opls_223 0.134 1
HA31 opls_140 0.000 1
HA32 opls_140 0.000 1
C opls_235 0.433 1
O opls_236 -1.316 1
C1 opls_558 0.340 1
CA1 opls_257 0.204 1
N opls_251 -0.838 1
CB1 opls_136 0.133 1
HB11 opls_140 0.000 1
HB12 opls_140 0.000 1
CG1 opls_136 0.133 1
HG11 opls_140 0.000 1
HG12 opls_140 0.000 1
CD3 opls_139 0.433 1
OE1 opls_235 -0.632 1
NE1 opls_237 0.127 1
HAE opls_909 0.072 1
HAD opls_909 0.072 1
[ bonds ]
CD1 CE1
CD1 HD11
CD1 CG2
CE1 CZ
CE1 HE11
CZ OH
CZ CE2
CE2 CD2
CE2 HE21
CD2 CG2
CD2 HD21
CG2 CB2
CB2 CA2
CB2 HB21
CA2 N2
CA2 C2
N2 C1
C2 O2
C2 N3
N3 CA3
N3 C1
CA3 C
CA3 HA31
CA3 HA32
C O
C1 CA1
CA1 N
CA1 CB1
CB1 CG1
CB1 HB11
CB1 HB12
CG1 CD3
CG1 HG11
CG1 HG12
CD3 OE1
CD3 NE1
NE1 HAE
NE1 HAD
-C N
[ impropers ]
CA +N C O improper_O_C_X_Y
***added to ffoplsaa.hdb
CRQ 9
1 1 CD1 CE1 CG2
1 1 CE1 OH CD1
1 1 CD2 CE2 CG2
1 1 CE2 OH CD2
1 1 CB2 CG2 CA2
2 6 CB1 CA1 CG1
2 6 CG1 CB1 CD3
2 3 NE1 CD3 OE1
2 6 CA3 N3 C
***added to aminoacids.dat
CRQ
when I run pdb2gmx on the pdb file 'pdb1mou.ent' (too large to be
Fatal error: Atom HE12 not found in rtp database in residue CRQ,
it looks a bit like HE11
pdb2gmx makes hydrogens by modifying the name of the atom it is bound
to. In your case you have NE1, so it wants to make HE12 and HE11. You
have however also a CE1. I would recommend to rename NE1 to NE2 and
thehydrogens to HE21 and HE22.
Did you also modify the ffoplsaa.hdb file?
Post by Dr Seth Carlton OLSEN
However, I am not sure why pdb2gmx is looking for this atom.
HE12 is not included in the pdb file (which, as expected, does not
contain hydrogens). Why is pdb2gmx looking for an atom that does
not exist and should not? Is there a naming convention in
operation of which I am not aware? Is pdb2gmx anticipating the
naming of the hydrogens to be put in the structure?
Post by Dr Seth Carlton OLSEN
If anyone has any insight into this problem, I would be very
grateful. For the moment, it has stopped me in my tracks.
Post by Dr Seth Carlton OLSEN
Cheers,
Seth
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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
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_______________________________________________
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Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr Seth Carlton OLSEN
2004-10-09 09:07:45 UTC
Permalink
Hi Gromacs Users,

Thanks David for that point. I have renamed NE1 to NE3 (since there is also a CE2) in the rtp, hdb files and in the pdb I'm trying to process. The fatal error then read:

Fatal error: Atom HE31 not found in rtp database in residue CRQ, it looks a bit like HE11

Accordingly, I changed the nitrogen-bonded hydrogen atoms (there should be 2) to HE31 and HE32 respectively. However, this generated the following fatal errors:

WARNING: atom HD11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HE11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HE11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HE21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HE21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HD21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom HB21 is missing in residue CRQ 62 in the pdb file
You might need to add atom HB21 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)


WARNING: atom O2 is missing in residue CRQ 62 in the pdb file

Fatal error: There were 6 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing

I have added the requisite lines to the hbd file, so I'm not sure why it does not find them. The hydrogens are not in the pdb file - I am adding them through the use of pdb2gmx. I'm not sure why it states that 02 is not in the pdb, since it is definitely there. Does pdb2gmx expect to find the hydrogens in the pdb file?

Cheers,

Seth

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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au

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----- Original Message -----
From: David <spoel at xray.bmc.uu.se>
Date: Saturday, October 9, 2004 6:37 pm
Subject: Re: [gmx-users] pdb2gmx problems and modified AA's
Post by Dr Seth Carlton OLSEN
Post by Dr Seth Carlton OLSEN
Hi Gromacs Users,
I am trying to run a pdb through pdb2gmx to get files to do an md
run. The protein chain contains an unconventional residue ('CRQ',
in the pdb). I am using the OPLS-AA forcefield. I have modified
the ffoplsaa.rtp, ffoplsaa.hdb and aminoacids.dat files by adding
Post by Dr Seth Carlton OLSEN
**added to ffoplsaa.rtp
;CRQ - chromophore GYQ from Rtms5 structure
[CRQ]
[ atoms ]
CD1 opls_145 0.029 1
HD11 opls_146 0.000 1
CE1 opls_145 0.030 1
HE11 opls_146 0.000 1
CZ opls_166 0.204 1
OH opls_167 -1.316 1
CE2 opls_145 0.029 1
HE21 opls_146 0.000 1
CD2 opls_145 0.029 1
HD21 opls_146 0.000 1
CG2 opls_145 0.050 1
CB2 opls_142 0.064 1
HB21 opls_144 0.000 1
CA2 opls_141 0.204 1
N2 opls_559 -0.436 1
C2 opls_235 0.340 1
O2 opls_236 -0.632 1
N3 opls_557 0.110 1
CA3 opls_223 0.134 1
HA31 opls_140 0.000 1
HA32 opls_140 0.000 1
C opls_235 0.433 1
O opls_236 -1.316 1
C1 opls_558 0.340 1
CA1 opls_257 0.204 1
N opls_251 -0.838 1
CB1 opls_136 0.133 1
HB11 opls_140 0.000 1
HB12 opls_140 0.000 1
CG1 opls_136 0.133 1
HG11 opls_140 0.000 1
HG12 opls_140 0.000 1
CD3 opls_139 0.433 1
OE1 opls_235 -0.632 1
NE1 opls_237 0.127 1
HAE opls_909 0.072 1
HAD opls_909 0.072 1
[ bonds ]
CD1 CE1
CD1 HD11
CD1 CG2
CE1 CZ
CE1 HE11
CZ OH
CZ CE2
CE2 CD2
CE2 HE21
CD2 CG2
CD2 HD21
CG2 CB2
CB2 CA2
CB2 HB21
CA2 N2
CA2 C2
N2 C1
C2 O2
C2 N3
N3 CA3
N3 C1
CA3 C
CA3 HA31
CA3 HA32
C O
C1 CA1
CA1 N
CA1 CB1
CB1 CG1
CB1 HB11
CB1 HB12
CG1 CD3
CG1 HG11
CG1 HG12
CD3 OE1
CD3 NE1
NE1 HAE
NE1 HAD
-C N
[ impropers ]
CA +N C O improper_O_C_X_Y
***added to ffoplsaa.hdb
CRQ 9
1 1 CD1 CE1 CG2
1 1 CE1 OH CD1
1 1 CD2 CE2 CG2
1 1 CE2 OH CD2
1 1 CB2 CG2 CA2
2 6 CB1 CA1 CG1
2 6 CG1 CB1 CD3
2 3 NE1 CD3 OE1
2 6 CA3 N3 C
***added to aminoacids.dat
CRQ
when I run pdb2gmx on the pdb file 'pdb1mou.ent' (too large to be
Fatal error: Atom HE12 not found in rtp database in residue CRQ,
it looks a bit like HE11
pdb2gmx makes hydrogens by modifying the name of the atom it is bound
to. In your case you have NE1, so it wants to make HE12 and HE11. You
have however also a CE1. I would recommend to rename NE1 to NE2 and
thehydrogens to HE21 and HE22.
Did you also modify the ffoplsaa.hdb file?
Post by Dr Seth Carlton OLSEN
However, I am not sure why pdb2gmx is looking for this atom.
HE12 is not included in the pdb file (which, as expected, does not
contain hydrogens). Why is pdb2gmx looking for an atom that does
not exist and should not? Is there a naming convention in
operation of which I am not aware? Is pdb2gmx anticipating the
naming of the hydrogens to be put in the structure?
Post by Dr Seth Carlton OLSEN
If anyone has any insight into this problem, I would be very
grateful. For the moment, it has stopped me in my tracks.
Post by Dr Seth Carlton OLSEN
Cheers,
Seth
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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gmx-users at gromacs.org
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Pawan Babel
2004-10-11 16:18:59 UTC
Permalink
Hi all
I am using OPLSAA forcefield with explicit water model on gromacs 3.2.1
with NAC & ACE terminal as capping my peptide chain.

During pdb2gmx i am getting following error :
Fatal error: Atom CH3 in residue NAC 15 not found in rtp entry with 6 atoms
while sorting atom

============details of my commands and procedure
[pawan at lysozyme helix]$ pdb2gmx -f pep.pdb -p pep.top -o pep.gro -inter -ignh
:-) G R O M A C S (-:

Glycine aRginine prOline Methionine Alanine Cystine Serine

:-) VERSION 3.2.1 (-:

Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
3
Looking whether force field file ffoplsaa.rtp exists
Opening library file /usr/local/share/gromacs/top/ffoplsaa.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading pep.pdb...
Read 119 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 15 residues with 119 atoms

chain #res #atoms
1 'A' 15 119

All occupancies are one
Opening library file /usr/local/share/gromacs/top/ffoplsaa.atp
Atomtype 700
Reading residue database... (ffoplsaa)
Opening library file /usr/local/share/gromacs/top/ffoplsaa.rtp
Residue 53
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/local/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /usr/local/share/gromacs/top/ffoplsaa-c.tdb

Back Off! I just backed up pep.top to ./#pep.top.8#
Processing chain 1 'A' (119 atoms, 15 residues)
Which LYSINE type do you want for residue 8
0. Not protonated (charge 0) (LYS)
1. Protonated (charge +1) (LYSH)

Type a number:1
Which ASPARTIC ACID type do you want for residue 7
0. Not protonated (charge -1) (ASP)
1. Protonated (charge 0) (ASPH)

Type a number:0
Which GLUTAMIC ACID type do you want for residue 2
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Type a number:0
Which GLUTAMIC ACID type do you want for residue 5
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Type a number:0
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Fatal error: Atom CH3 in residue NAC 15 not found in rtp entry with 6 atoms
while sorting atoms
================================================================== Now i
check my defualt entry of ffoplsaa files in .../gromacs/top
directory.

Default entry in ffoplsaa.hdb for ACE and NAC in gromacs 3.2.1 are : NAC
2
1 1 N -C CH3
3 4 CH3 N -C

ACE 1
3 4 CH3 C O
=========================================
and default entry in ffoplsaa.itp for ACE and NAC are:
[ ACE ]
[ atoms ]
CA opls_135 -0.180 1
HH31 opls_140 0.060 1
HH32 opls_140 0.060 1
HH33 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
CA HH31
CA HH32
CA HH33
CA C
C O
[ impropers ]
CA +N C O improper_O_C_X_Y

[ NAC ] ; metylamide, a.k.a NMA.
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_242 0.020 2
HH31 opls_140 0.060 2
HH32 opls_140 0.060 2
HH33 opls_140 0.060 2
[ bonds ]
N H
N CA
CA HH31
CA HH32
CA HH33
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
===========================================================
But can anyone explain me why there are different nomenclature in
ffoplsaa.hdb and ffoplsaa.itp ?

seeing different nomenclature used in ffoplsaa.hdb and ffoplsaa.itp for
alpha carbon. So i modified the my ffoplsaa.rtp file by replacing CA by
CH3.
Now it does not any error during pdb2gmx but it shows error during grompp.
WARNING 1 [file "pep.top", line 1551]:
No default Ryckaert-Bell. types, using zeroes
WARNING 2 [file "pep.top", line 2161]:
No default Ryckaert-Bell. types, using zeroe

My modified ffoplsaa.rtp with ACE and NAC as :
===================ffoplsaa.rtp ------------
[ ACE ]
[ atoms ]
CH3 opls_135 -0.180 1
HH31 opls_140 0.060 1
HH32 opls_140 0.060 1
HH33 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
CH3 HH31
CH3 HH32
CH3 HH33
CH3 C
C O
[ impropers ]
CH3 +N C O improper_O_C_X_Y


[ NAC ] ; metylamide, a.k.a NMA.
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CH3 opls_242 0.020 2
HH31 opls_140 0.060 2
HH32 opls_140 0.060 2
HH33 opls_140 0.060 2
[ bonds ]
N H
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
-C N
[ impropers ]
-C CH3 N H improper_Z_N_X_Y
======================================================

Any help is greatly appreciated.
Thanks
Pawan Babel
Anton Feenstra
2004-10-12 16:05:37 UTC
Permalink
Post by Pawan Babel
Hi all
I am using OPLSAA forcefield with explicit water model on gromacs 3.2.1
with NAC & ACE terminal as capping my peptide chain.
Fatal error: Atom CH3 in residue NAC 15 not found in rtp entry with 6 atoms
while sorting atom
[...]

Entries in the .hdb should be atom *names*, it seems that by mistake
the atom *types* were entered. The CH3 probably should be CA, and you
should check the others as well.
Post by Pawan Babel
NAC 2
1 1 N -C CH3
3 4 CH3 N -C
ACE 1
3 4 CH3 C O
=========================================
[ ACE ]
[ atoms ]
CA opls_135 -0.180 1
HH31 opls_140 0.060 1
HH32 opls_140 0.060 1
HH33 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[...]
--
Groetjes,

Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
|_____________|_______________________________________________________|
Anton Feenstra
2004-10-12 16:01:54 UTC
Permalink
Post by Dr Seth Carlton OLSEN
Hi Gromacs Users,
Fatal error: Atom HE31 not found in rtp database in residue CRQ, it looks a bit like HE11
WARNING: atom HD11 is missing in residue CRQ 62 in the pdb file
You might need to add atom HD11 to the hydrogen database of residue CRQ in the file ff???.hdb (see the manual)
Did you also rename the atoms in the ffoplsaa.hdb?
The atom names must match exactly between .pdb (or .ent), .rtp and .hdb.
Atom names for the added H's are generated from the 'bonded' N or C, so
the H to CD1 will be HD11 and HD12.
--
Groetjes,

Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
|_____________|_______________________________________________________|
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