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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 21 16:05:44 CEST 2010


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
>>          >
>>          > ========================================
>>          > --
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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
>>
>>     ========================================
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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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