[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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>>>>
>>>>
>>>> -- ========================================
>>>>
>>>> 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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>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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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