[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
>>> >
>>> > ========================================
>>> > --
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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
>>>
>>> ========================================
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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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--
Dr Thomas Piggot
University of Southampton, UK.
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