[gmx-users] Problem with pdb2gmx and a new residue
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 21 00:00:40 CEST 2010
Mark Abraham wrote:
>
>
> ----- Original Message -----
> From: "Justin A. Lemkul" <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>
>
> >
> > 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 | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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