Re: [gmx-users] Problem with pdb2gmx and a new residue
Thomas Piggot wrote:
Hi,
If I'm not mistaken then I think pdb2gmx is renaming O2 to OXT because
of changes to the entries in the xlateat.dat file (found in the top
folder).
Good point, thanks. I still think it would be a useful improvement if pdb2gmx
double-checked itself. Since that particular translation is only intended for
C-termini, then my case (which I suspect will be shared by many others) still
causes an annoying failure.
-Justin
Cheers
Tom
Justin A. Lemkul wrote:
I have posted a work-around in the discussion of bug #567. I think a
code fix
will still be preferable, ultimately, but if you're stuck, you can
give it a try.
http://bugzilla.gromacs.org/show_bug.cgi?id=567
-Justin
Justin A. Lemkul wrote:
Ramachandran G wrote:
Hi Justin,
Presently i too facing the same exact problem. I built the
topology for a chromophore in the protein and entered all the new
parameters in the .rtp, atp, hdb and defined the bonded and nonbonded
parameters. Finally i got the following error.
Fatal error:
Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27
atoms
while sorting atoms.
By this time if you identified the problem. Please help me too. Thank
you.
I have filed a bugzilla. If I can help the developers further diagnose
the issue I will, but until that time, I'm awaiting a patch.
-Justin
Rama
On Mon, Sep 20, 2010 at 3:00 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:
Mark Abraham wrote:
- Original Message -
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Date: Tuesday, September 21, 2010 6:30
Subject: [gmx-users] Problem with pdb2gmx and a new residue
To: Gromacs Users' List mailto:gmx-users@gromacs.org>>
>
> Hi All,
>
> I'm trying to build a topology for a chromophore-containing
> protein using Gromacs 4.5 and OPLS-AA. The chromophore is
> incorporated into the protein's backbone and the parameters
all
> come from a reputable publication, so I've done the
following:
>
> 1. Created a new .rtp entry
> 2. Created an .hdb entry
> 3. Defined all nonbonded parameters for new atomtypes in the
> .atp and ffnonbonded.itp file
> 4. Defined all new bonded parameters in ffbonded.itp
I think you need to define CRO as Protein in
residuetypes.dat so
that the pdb2gmx mechanism can deduce that it should form a
C-terminal peptide link in the absence of an end-of-chain
marker.
I had done that, I forgot to mention it. I tried using my modified
residuetypes.dat from both the working directory and in $GMXLIB.
Similarly, I have a modified peptide in what's become my
"system
for generating pdb2gmx bugzilla reports", and with 4.5.1 and
git
head, if I omit the residuetypes.dat definition I see
Identified residue ALA1 as a starting terminus.
Warning: Residue KCX193 in chain has different type (Other)
from
starting residue ALA1 (Protein).
Warning: Residue ASP194 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASP195 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue GLU196 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASN197 in chain has different type (Protein)
from starting residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling
further warnings.
Identified residue THR192 as a ending terminus.
---
Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340
Source code file: ../../../src/kernel/pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue VAL 467 was not found in rtp entry VAL with
16 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
This is a bit different, inasmuch as I see the error on the
final residue of the first chain, rather then on the modified
residue, as you do. However pdb2gmx should cope better with
this
case - clearly it's confused in the above messages about
non-matching types.
We should probably file a bugzilla, even if this fixes your
symptoms.
I figured as much, just thought I'd check to see if I'd missed
anything obvious. Thanks for the reply. I'll file a bugzilla.
-Justin
Mark
>
Re: [gmx-users] Problem with pdb2gmx and a new residue
Hi,
If I'm not mistaken then I think pdb2gmx is renaming O2 to OXT because
of changes to the entries in the xlateat.dat file (found in the top folder).
Cheers
Tom
Justin A. Lemkul wrote:
I have posted a work-around in the discussion of bug #567. I think a code fix
will still be preferable, ultimately, but if you're stuck, you can give it a
try.
http://bugzilla.gromacs.org/show_bug.cgi?id=567
-Justin
Justin A. Lemkul wrote:
Ramachandran G wrote:
Hi Justin,
Presently i too facing the same exact problem. I built the
topology for a chromophore in the protein and entered all the new
parameters in the .rtp, atp, hdb and defined the bonded and nonbonded
parameters. Finally i got the following error.
Fatal error:
Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27 atoms
while sorting atoms.
By this time if you identified the problem. Please help me too. Thank
you.
I have filed a bugzilla. If I can help the developers further diagnose
the issue I will, but until that time, I'm awaiting a patch.
-Justin
Rama
On Mon, Sep 20, 2010 at 3:00 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:
Mark Abraham wrote:
- Original Message -
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Date: Tuesday, September 21, 2010 6:30
Subject: [gmx-users] Problem with pdb2gmx and a new residue
To: Gromacs Users' List mailto:gmx-users@gromacs.org>>
>
> Hi All,
>
> I'm trying to build a topology for a chromophore-containing
> protein using Gromacs 4.5 and OPLS-AA. The chromophore is
> incorporated into the protein's backbone and the parameters
all
> come from a reputable publication, so I've done the following:
>
> 1. Created a new .rtp entry
> 2. Created an .hdb entry
> 3. Defined all nonbonded parameters for new atomtypes in the
> .atp and ffnonbonded.itp file
> 4. Defined all new bonded parameters in ffbonded.itp
I think you need to define CRO as Protein in residuetypes.dat so
that the pdb2gmx mechanism can deduce that it should form a
C-terminal peptide link in the absence of an end-of-chain marker.
I had done that, I forgot to mention it. I tried using my modified
residuetypes.dat from both the working directory and in $GMXLIB.
Similarly, I have a modified peptide in what's become my "system
for generating pdb2gmx bugzilla reports", and with 4.5.1 and git
head, if I omit the residuetypes.dat definition I see
Identified residue ALA1 as a starting terminus.
Warning: Residue KCX193 in chain has different type (Other) from
starting residue ALA1 (Protein).
Warning: Residue ASP194 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASP195 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue GLU196 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASN197 in chain has different type (Protein)
from starting residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling
further warnings.
Identified residue THR192 as a ending terminus.
---
Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340
Source code file: ../../../src/kernel/pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue VAL 467 was not found in rtp entry VAL with
16 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
This is a bit different, inasmuch as I see the error on the
final residue of the first chain, rather then on the modified
residue, as you do. However pdb2gmx should cope better with this
case - clearly it's confused in the above messages about
non-matching types.
We should probably file a bugzilla, even if this fixes your
symptoms.
I figured as much, just thought I'd check to see if I'd missed
anything obvious. Thanks for the reply. I'll file a bugzilla.
-Justin
Mark
> The coordinate file was then input into pdb2gmx with an
> oplsaa.ff directory in the working directory. I received
> the following error (identical with version 4.5 and the most
> recent git with release-4-5-patches):
>
> pdb2gmx -f struct.pdb
>
Re: [gmx-users] Problem with pdb2gmx and a new residue
I have posted a work-around in the discussion of bug #567. I think a code fix
will still be preferable, ultimately, but if you're stuck, you can give it a try.
http://bugzilla.gromacs.org/show_bug.cgi?id=567
-Justin
Justin A. Lemkul wrote:
Ramachandran G wrote:
Hi Justin,
Presently i too facing the same exact problem. I built the
topology for a chromophore in the protein and entered all the new
parameters in the .rtp, atp, hdb and defined the bonded and nonbonded
parameters. Finally i got the following error.
Fatal error:
Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27 atoms
while sorting atoms.
By this time if you identified the problem. Please help me too. Thank
you.
I have filed a bugzilla. If I can help the developers further diagnose
the issue I will, but until that time, I'm awaiting a patch.
-Justin
Rama
On Mon, Sep 20, 2010 at 3:00 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Mark Abraham wrote:
- Original Message -
From: "Justin A. Lemkul" <mailto:jalem...@vt.edu>>
Date: Tuesday, September 21, 2010 6:30
Subject: [gmx-users] Problem with pdb2gmx and a new residue
To: Gromacs Users' List mailto:gmx-users@gromacs.org>>
>
> Hi All,
>
> I'm trying to build a topology for a chromophore-containing
> protein using Gromacs 4.5 and OPLS-AA. The chromophore is
> incorporated into the protein's backbone and the parameters
all
> come from a reputable publication, so I've done the following:
>
> 1. Created a new .rtp entry
> 2. Created an .hdb entry
> 3. Defined all nonbonded parameters for new atomtypes in the
> .atp and ffnonbonded.itp file
> 4. Defined all new bonded parameters in ffbonded.itp
I think you need to define CRO as Protein in residuetypes.dat so
that the pdb2gmx mechanism can deduce that it should form a
C-terminal peptide link in the absence of an end-of-chain marker.
I had done that, I forgot to mention it. I tried using my modified
residuetypes.dat from both the working directory and in $GMXLIB.
Similarly, I have a modified peptide in what's become my "system
for generating pdb2gmx bugzilla reports", and with 4.5.1 and git
head, if I omit the residuetypes.dat definition I see
Identified residue ALA1 as a starting terminus.
Warning: Residue KCX193 in chain has different type (Other) from
starting residue ALA1 (Protein).
Warning: Residue ASP194 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASP195 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue GLU196 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASN197 in chain has different type (Protein)
from starting residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling
further warnings.
Identified residue THR192 as a ending terminus.
---
Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340
Source code file: ../../../src/kernel/pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue VAL 467 was not found in rtp entry VAL with
16 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
This is a bit different, inasmuch as I see the error on the
final residue of the first chain, rather then on the modified
residue, as you do. However pdb2gmx should cope better with this
case - clearly it's confused in the above messages about
non-matching types.
We should probably file a bugzilla, even if this fixes your
symptoms.
I figured as much, just thought I'd check to see if I'd missed
anything obvious. Thanks for the reply. I'll file a bugzilla.
-Justin
Mark
> The coordinate file was then input into pdb2gmx with an
> oplsaa.ff directory in the working directory. I received
> the following error (identical with version 4.5 and the most
> recent git with release-4-5-patches):
>
> pdb2gmx -f struct.pdb
> ...
> ---
> Program pdb2gmx, VERSION 4.5.1-20100920-03d181e
> Source code file: pdb2gmx.c, line
Re: [gmx-users] Problem with pdb2gmx and a new residue
Ramachandran G wrote:
Hi Justin,
Presently i too facing the same exact problem. I built the topology
for a chromophore in the protein and entered all the new parameters in
the .rtp, atp, hdb and defined the bonded and nonbonded parameters.
Finally i got the following error.
Fatal error:
Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27 atoms
while sorting atoms.
By this time if you identified the problem. Please help me too. Thank you.
I have filed a bugzilla. If I can help the developers further diagnose the
issue I will, but until that time, I'm awaiting a patch.
-Justin
Rama
On Mon, Sep 20, 2010 at 3:00 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Mark Abraham wrote:
- Original Message -
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Date: Tuesday, September 21, 2010 6:30
Subject: [gmx-users] Problem with pdb2gmx and a new residue
To: Gromacs Users' List mailto:gmx-users@gromacs.org>>
>
> Hi All,
>
> I'm trying to build a topology for a chromophore-containing
> protein using Gromacs 4.5 and OPLS-AA. The chromophore is
> incorporated into the protein's backbone and the parameters all
> come from a reputable publication, so I've done the following:
>
> 1. Created a new .rtp entry
> 2. Created an .hdb entry
> 3. Defined all nonbonded parameters for new atomtypes in the
> .atp and ffnonbonded.itp file
> 4. Defined all new bonded parameters in ffbonded.itp
I think you need to define CRO as Protein in residuetypes.dat so
that the pdb2gmx mechanism can deduce that it should form a
C-terminal peptide link in the absence of an end-of-chain marker.
I had done that, I forgot to mention it. I tried using my modified
residuetypes.dat from both the working directory and in $GMXLIB.
Similarly, I have a modified peptide in what's become my "system
for generating pdb2gmx bugzilla reports", and with 4.5.1 and git
head, if I omit the residuetypes.dat definition I see
Identified residue ALA1 as a starting terminus.
Warning: Residue KCX193 in chain has different type (Other) from
starting residue ALA1 (Protein).
Warning: Residue ASP194 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASP195 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue GLU196 in chain has different type (Protein)
from starting residue ALA1 (Protein).
Warning: Residue ASN197 in chain has different type (Protein)
from starting residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling
further warnings.
Identified residue THR192 as a ending terminus.
---
Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340
Source code file: ../../../src/kernel/pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue VAL 467 was not found in rtp entry VAL with
16 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
This is a bit different, inasmuch as I see the error on the
final residue of the first chain, rather then on the modified
residue, as you do. However pdb2gmx should cope better with this
case - clearly it's confused in the above messages about
non-matching types.
We should probably file a bugzilla, even if this fixes your
symptoms.
I figured as much, just thought I'd check to see if I'd missed
anything obvious. Thanks for the reply. I'll file a bugzilla.
-Justin
Mark
> The coordinate file was then input into pdb2gmx with an
> oplsaa.ff directory in the working directory. I received
> the following error (identical with version 4.5 and the most
> recent git with release-4-5-patches):
>
> pdb2gmx -f struct.pdb
> ...
> ---
> Program pdb2gmx, VERSION 4.5.1-20100920-03d181e
> Source code file: pdb2gmx.c, line: 655
>
> Fatal error:
> Atom OXT in residue CRO 331 was not found in rtp entry CRO with
> 39 atoms
> while sorting atoms.
Re: [gmx-users] Problem with pdb2gmx and a new residue
Hi Justin, Presently i too facing the same exact problem. I built the topology for a chromophore in the protein and entered all the new parameters in the .rtp, atp, hdb and defined the bonded and nonbonded parameters. Finally i got the following error. Fatal error: Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27 atoms while sorting atoms. By this time if you identified the problem. Please help me too. Thank you. Rama On Mon, Sep 20, 2010 at 3:00 PM, Justin A. Lemkul wrote: > > > Mark Abraham wrote: > >> >> >> - Original Message - >> From: "Justin A. Lemkul" >> Date: Tuesday, September 21, 2010 6:30 >> Subject: [gmx-users] Problem with pdb2gmx and a new residue >> To: Gromacs Users' List >> >> > >> > Hi All, >> > >> > I'm trying to build a topology for a chromophore-containing >> > protein using Gromacs 4.5 and OPLS-AA. The chromophore is >> > incorporated into the protein's backbone and the parameters all >> > come from a reputable publication, so I've done the following: >> > >> > 1. Created a new .rtp entry >> > 2. Created an .hdb entry >> > 3. Defined all nonbonded parameters for new atomtypes in the >> > .atp and ffnonbonded.itp file >> > 4. Defined all new bonded parameters in ffbonded.itp >> >> I think you need to define CRO as Protein in residuetypes.dat so that the >> pdb2gmx mechanism can deduce that it should form a C-terminal peptide link >> in the absence of an end-of-chain marker. >> >> > I had done that, I forgot to mention it. I tried using my modified > residuetypes.dat from both the working directory and in $GMXLIB. > > Similarly, I have a modified peptide in what's become my "system for >> generating pdb2gmx bugzilla reports", and with 4.5.1 and git head, if I omit >> the residuetypes.dat definition I see >> >> Identified residue ALA1 as a starting terminus. >> Warning: Residue KCX193 in chain has different type (Other) from starting >> residue ALA1 (Protein). >> Warning: Residue ASP194 in chain has different type (Protein) from >> starting residue ALA1 (Protein). >> Warning: Residue ASP195 in chain has different type (Protein) from >> starting residue ALA1 (Protein). >> Warning: Residue GLU196 in chain has different type (Protein) from >> starting residue ALA1 (Protein). >> Warning: Residue ASN197 in chain has different type (Protein) from >> starting residue ALA1 (Protein). >> More than 5 unidentified residues at end of chain - disabling further >> warnings. >> Identified residue THR192 as a ending terminus. >> >> --- >> Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 >> Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 >> >> Fatal error: >> Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms >> while sorting atoms. >> . >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> >> This is a bit different, inasmuch as I see the error on the final residue >> of the first chain, rather then on the modified residue, as you do. However >> pdb2gmx should cope better with this case - clearly it's confused in the >> above messages about non-matching types. >> >> We should probably file a bugzilla, even if this fixes your symptoms. >> >> > I figured as much, just thought I'd check to see if I'd missed anything > obvious. Thanks for the reply. I'll file a bugzilla. > > -Justin > > Mark >> > The coordinate file was then input into pdb2gmx with an >> > oplsaa.ff directory in the working directory. I received >> > the following error (identical with version 4.5 and the most >> > recent git with release-4-5-patches): >> > >> > pdb2gmx -f struct.pdb >> > ... >> > --- >> > Program pdb2gmx, VERSION 4.5.1-20100920-03d181e >> > Source code file: pdb2gmx.c, line: 655 >> > >> > Fatal error: >> > Atom OXT in residue CRO 331 was not found in rtp entry CRO with >> > 39 atoms >> > while sorting atoms. >> > . >> > For more information and tips for troubleshooting, please check >> > the GROMACS >> > website at http://www.gromacs.org/Documentation/Errors
Re: [gmx-users] Problem with pdb2gmx and a new residue
Mark Abraham wrote: - Original Message - From: "Justin A. Lemkul" Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List > > Hi All, > > I'm trying to build a topology for a chromophore-containing > protein using Gromacs 4.5 and OPLS-AA. The chromophore is > incorporated into the protein's backbone and the parameters all > come from a reputable publication, so I've done the following: > > 1. Created a new .rtp entry > 2. Created an .hdb entry > 3. Defined all nonbonded parameters for new atomtypes in the > .atp and ffnonbonded.itp file > 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. I had done that, I forgot to mention it. I tried using my modified residuetypes.dat from both the working directory and in $GMXLIB. Similarly, I have a modified peptide in what's become my "system for generating pdb2gmx bugzilla reports", and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. I figured as much, just thought I'd check to see if I'd missed anything obvious. Thanks for the reply. I'll file a bugzilla. -Justin Mark > The coordinate file was then input into pdb2gmx with an > oplsaa.ff directory in the working directory. I received > the following error (identical with version 4.5 and the most > recent git with release-4-5-patches): > > pdb2gmx -f struct.pdb > ... > --- > Program pdb2gmx, VERSION 4.5.1-20100920-03d181e > Source code file: pdb2gmx.c, line: 655 > > Fatal error: > Atom OXT in residue CRO 331 was not found in rtp entry CRO with > 39 atoms > while sorting atoms. > . > For more information and tips for troubleshooting, please check > the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > The CRO residue is my chromophore. I'm wondering why > pdb2gmx is finding an OXT atom in the following coordinates: > > ... > ATOM 2528 N LEU A > 330 -13.640 10.888 -25.907 > 1.00 0.00 > ATOM 2529 CA LEU A > 330 -12.513 11.013 -26.852 > 1.00 0.00 > ATOM 2530 C LEU A > 330 -11.281 10.183 -26.416 > 1.00 0.00 > ATOM 2531 O LEU A > 330 -10.625 9.588 - > 27.277 1.00 0.00 > ATOM 2532 CB LEU A > 330 -12.159 12.493 -27.066 > 1.00 0.00 > ATOM 2533 CG LEU A > 330 -13.206 13.415 -27.691 > 1.00 0.00 > ATOM 2534 CD1 LEU A > 330 -12.913 14.905 -27.393 > 1.00 0.00 > ATOM 2535 CD2 LEU A > 330 -13.400 13.160 -29.207 > 1.00 0.00 > ATOM 2536 N CRO A > 331 -10.669 9.142 - > 25.611 1.00 0.00 > ATOM 2537 CE CRO A > 331 -7.407 12.564 - > 27.240 1.00 0.00 > ATOM 2538 SD CRO A > 331 -8.035 12.603 - > 25.595 1.00 0.00 > ATOM 2539 CG1 CRO A > 331 -8.731 10.996 - > 25.519 1.00 0.00 > ATOM 2540 CB1 CRO A > 331 -9.6
Re: [gmx-users] Problem with pdb2gmx and a new residue
- Original Message - From: "Justin A. Lemkul" Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List > > Hi All, > > I'm trying to build a topology for a chromophore-containing > protein using Gromacs 4.5 and OPLS-AA. The chromophore is > incorporated into the protein's backbone and the parameters all > come from a reputable publication, so I've done the following: > > 1. Created a new .rtp entry > 2. Created an .hdb entry > 3. Defined all nonbonded parameters for new atomtypes in the > .atp and ffnonbonded.itp file > 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. Similarly, I have a modified peptide in what's become my "system for generating pdb2gmx bugzilla reports", and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. Mark > The coordinate file was then input into pdb2gmx with an > oplsaa.ff directory in the working directory. I received > the following error (identical with version 4.5 and the most > recent git with release-4-5-patches): > > pdb2gmx -f struct.pdb > ... > --- > Program pdb2gmx, VERSION 4.5.1-20100920-03d181e > Source code file: pdb2gmx.c, line: 655 > > Fatal error: > Atom OXT in residue CRO 331 was not found in rtp entry CRO with > 39 atoms > while sorting atoms. > . > For more information and tips for troubleshooting, please check > the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > The CRO residue is my chromophore. I'm wondering why > pdb2gmx is finding an OXT atom in the following coordinates: > > ... > ATOM 2528 N LEU A > 330 -13.640 10.888 -25.907 > 1.00 0.00 > ATOM 2529 CA LEU A > 330 -12.513 11.013 -26.852 > 1.00 0.00 > ATOM 2530 C LEU A > 330 -11.281 10.183 -26.416 > 1.00 0.00 > ATOM 2531 O LEU A > 330 -10.625 9.588 - > 27.277 1.00 0.00 > ATOM 2532 CB LEU A > 330 -12.159 12.493 -27.066 > 1.00 0.00 > ATOM 2533 CG LEU A > 330 -13.206 13.415 -27.691 > 1.00 0.00 > ATOM 2534 CD1 LEU A > 330 -12.913 14.905 -27.393 > 1.00 0.00 > ATOM 2535 CD2 LEU A > 330 -13.400 13.160 -29.207 > 1.00 0.00 > ATOM 2536 N CRO A > 331 -10.669 9.142 - > 25.611 1.00 0.00 > ATOM 2537 CE CRO A > 331 -7.407 12.564 - > 27.240 1.00 0.00 > ATOM 2538 SD CRO A > 331 -8.035 12.603 - > 25.595 1.00 0.00 > ATOM 2539 CG1 CRO A > 331 -8.731 10.996 - > 25.519 1.00 0.00 > ATOM 2540 CB1 CRO A > 331 -9.618 10.846 - > 24.279 1.00 0.00 > ATOM 2541 CA1 CRO A > 331 -10.227 9.470 - > 24.406 1.00 0.00 > ATOM 2542 C1 CRO A > 331 -10.304 8.516 - > 23.260 1.00 0.00 > ATOM 2543 N2 CRO A > 331 -9.873 8.765 - > 21.981 1.00 0.00 > ATOM 2544 OH CRO A > 331 -8.594 11.111 - > 15.969 1.00 0.00 &g
Re: [gmx-users] Problem with pdb2gmx and a new residue
- Original Message - From: "Justin A. Lemkul" Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List > > Hi All, > > I'm trying to build a topology for a chromophore-containing > protein using Gromacs 4.5 and OPLS-AA. The chromophore is > incorporated into the protein's backbone and the parameters all > come from a reputable publication, so I've done the following: > > 1. Created a new .rtp entry > 2. Created an .hdb entry > 3. Defined all nonbonded parameters for new atomtypes in the > .atp and ffnonbonded.itp file > 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. Similarly, I have a modified peptide in what's become my "system for generating pdb2gmx bugzilla reports", and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. Mark > The coordinate file was then input into pdb2gmx with an > oplsaa.ff directory in the working directory. I received > the following error (identical with version 4.5 and the most > recent git with release-4-5-patches): > > pdb2gmx -f struct.pdb > ... > --- > Program pdb2gmx, VERSION 4.5.1-20100920-03d181e > Source code file: pdb2gmx.c, line: 655 > > Fatal error: > Atom OXT in residue CRO 331 was not found in rtp entry CRO with > 39 atoms > while sorting atoms. > . > For more information and tips for troubleshooting, please check > the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > The CRO residue is my chromophore. I'm wondering why > pdb2gmx is finding an OXT atom in the following coordinates: > > ... > ATOM 2528 N LEU A > 330 -13.640 10.888 -25.907 > 1.00 0.00 > ATOM 2529 CA LEU A > 330 -12.513 11.013 -26.852 > 1.00 0.00 > ATOM 2530 C LEU A > 330 -11.281 10.183 -26.416 > 1.00 0.00 > ATOM 2531 O LEU A > 330 -10.625 9.588 - > 27.277 1.00 0.00 > ATOM 2532 CB LEU A > 330 -12.159 12.493 -27.066 > 1.00 0.00 > ATOM 2533 CG LEU A > 330 -13.206 13.415 -27.691 > 1.00 0.00 > ATOM 2534 CD1 LEU A > 330 -12.913 14.905 -27.393 > 1.00 0.00 > ATOM 2535 CD2 LEU A > 330 -13.400 13.160 -29.207 > 1.00 0.00 > ATOM 2536 N CRO A > 331 -10.669 9.142 - > 25.611 1.00 0.00 > ATOM 2537 CE CRO A > 331 -7.407 12.564 - > 27.240 1.00 0.00 > ATOM 2538 SD CRO A > 331 -8.035 12.603 - > 25.595 1.00 0.00 > ATOM 2539 CG1 CRO A > 331 -8.731 10.996 - > 25.519 1.00 0.00 > ATOM 2540 CB1 CRO A > 331 -9.618 10.846 - > 24.279 1.00 0.00 > ATOM 2541 CA1 CRO A > 331 -10.227 9.470 - > 24.406 1.00 0.00 > ATOM 2542 C1 CRO A > 331 -10.304 8.516 - > 23.260 1.00 0.00 > ATOM 2543 N2 CRO A > 331 -9.873 8.765 - > 21.981 1.00 0.00 > ATOM 2544 OH CRO A >
[gmx-users] Problem with pdb2gmx and a new residue
Hi All, I'm trying to build a topology for a chromophore-containing protein using Gromacs 4.5 and OPLS-AA. The chromophore is incorporated into the protein's backbone and the parameters all come from a reputable publication, so I've done the following: 1. Created a new .rtp entry 2. Created an .hdb entry 3. Defined all nonbonded parameters for new atomtypes in the .atp and ffnonbonded.itp file 4. Defined all new bonded parameters in ffbonded.itp The coordinate file was then input into pdb2gmx with an oplsaa.ff directory in the working directory. I received the following error (identical with version 4.5 and the most recent git with release-4-5-patches): pdb2gmx -f struct.pdb ... --- Program pdb2gmx, VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue CRO 331 was not found in rtp entry CRO with 39 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The CRO residue is my chromophore. I'm wondering why pdb2gmx is finding an OXT atom in the following coordinates: ... ATOM 2528 N LEU A 330 -13.640 10.888 -25.907 1.00 0.00 ATOM 2529 CA LEU A 330 -12.513 11.013 -26.852 1.00 0.00 ATOM 2530 C LEU A 330 -11.281 10.183 -26.416 1.00 0.00 ATOM 2531 O LEU A 330 -10.625 9.588 -27.277 1.00 0.00 ATOM 2532 CB LEU A 330 -12.159 12.493 -27.066 1.00 0.00 ATOM 2533 CG LEU A 330 -13.206 13.415 -27.691 1.00 0.00 ATOM 2534 CD1 LEU A 330 -12.913 14.905 -27.393 1.00 0.00 ATOM 2535 CD2 LEU A 330 -13.400 13.160 -29.207 1.00 0.00 ATOM 2536 N CRO A 331 -10.669 9.142 -25.611 1.00 0.00 ATOM 2537 CE CRO A 331 -7.407 12.564 -27.240 1.00 0.00 ATOM 2538 SD CRO A 331 -8.035 12.603 -25.595 1.00 0.00 ATOM 2539 CG1 CRO A 331 -8.731 10.996 -25.519 1.00 0.00 ATOM 2540 CB1 CRO A 331 -9.618 10.846 -24.279 1.00 0.00 ATOM 2541 CA1 CRO A 331 -10.227 9.470 -24.406 1.00 0.00 ATOM 2542 C1 CRO A 331 -10.304 8.516 -23.260 1.00 0.00 ATOM 2543 N2 CRO A 331 -9.873 8.765 -21.981 1.00 0.00 ATOM 2544 OH CRO A 331 -8.594 11.111 -15.969 1.00 0.00 ATOM 2545 CD2 CRO A 331 -9.219 9.756 -19.205 1.00 0.00 ATOM 2546 CE2 CRO A 331 -8.888 10.677 -18.207 1.00 0.00 ATOM 2547 CZ CRO A 331 -8.898 10.286 -16.863 1.00 0.00 ATOM 2548 CE1 CRO A 331 -9.219 8.975 -16.518 1.00 0.00 ATOM 2549 CD1 CRO A 331 -9.549 8.056 -17.509 1.00 0.00 ATOM 2550 CG2 CRO A 331 -9.557 8.447 -18.848 1.00 0.00 ATOM 2551 CB2 CRO A 331 -9.880 7.417 -19.857 1.00 0.00 ATOM 2552 CA2 CRO A 331 -10.149 7.645 -21.293 1.00 0.00 ATOM 2553 C2 CRO A 331 -10.726 6.753 -22.143 1.00 0.00 ATOM 2554 O2 CRO A 331 -11.108 5.574 -21.819 1.00 0.00 ATOM 2555 N3 CRO A 331 -10.810 7.255 -23.355 1.00 0.00 ATOM 2556 CA3 CRO A 331 -11.435 6.545 -24.488 1.00 0.00 ATOM 2557 C CRO A 331 -10.492 6.111 -25.580 1.00 0.00 ATOM 2558 O CRO A 331 -10.993 5.596 -26.570 1.00 0.00 ATOM 2559 N VAL A 332 -9.265 5.813 -25.096 1.00 0.00 ATOM 2560 CA VAL A 332 -8.235 4.899 -25.607 1.00 0.00 ATOM 2561 C VAL A 332 -7.512 4.308 -24.397 1.00 0.00 ATOM 2562 O VAL A 332 -6.351 4.567 -24.155 1.00 0.00 ATOM 2563 CB VAL A 332 -7.312 5.633 -26.627 1.00 0.00 ATOM 2564 CG1 VAL A 332 -8.127 5.980 -27.896 1.00 0.00 ATOM 2565 CG2 VAL A 332 -6.687 6.887 -26.051 1.00 0.00 ... Any ideas on what's going on? I can upload a bugzilla if necessary, I just thought I'd report here first since I'm not sure if I'm doing something wrong with respect to the many new pdb2gmx features. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
