[gmx-users] Problem with pdb2gmx and a new residue
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 20 22:29:10 CEST 2010
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
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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