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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 21 16:37:13 CEST 2010



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 <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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>>>>         <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
>>>>     <mailto:gmx-users at gromacs.org>
>>>>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>     Please search the archive at
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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
>>
>> ========================================
>> -- 
>> gmx-users mailing list    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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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



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