[gmx-users] Problem with pdb2gmx and a new residue

Thomas Piggot t.piggot at soton.ac.uk
Tue Sep 21 16:31:07 CEST 2010


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 <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>>     Mark Abraham wrote:
>>>
>>>
>>>
>>>         ----- Original Message -----
>>>         From: "Justin A. Lemkul" <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>>
>>>         Date: Tuesday, September 21, 2010 6:30
>>>         Subject: [gmx-users] Problem with pdb2gmx and a new residue
>>>         To: Gromacs Users' List <gmx-users at gromacs.org
>>>         <mailto:gmx-users at 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.
>>>         <snip>
>>>         -------------------------------------------------------
>>>         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      -9.618  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 <http://vt.edu> | (540) 231-9080
>>>          > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>          >
>>>          > ========================================
>>>          > --
>>>          > gmx-users mailing list    gmx-users at gromacs.org
>>>         <mailto:gmx-users at gromacs.org>
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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> | (540) 231-9080
>>>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>     ========================================
>>>     --     gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>>
>>>
>>>
>>> --
>>> Postdoctoral Research Scholar,
>>> Department of Chemistry,
>>> University of Nevada, Reno.
> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> --
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-- 
Dr Thomas Piggot
University of Southampton, UK.



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