[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
>> >
>> > ========================================
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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