Mark Abraham wrote:
----- Original Message -----
From: "Justin A. Lemkul" <jalem...@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@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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