[gmx-users] Problem with encad in pdb2gmx, GMX 3.3 CVS version

[Leonardo Sepulveda Durán]

Hello!!

I downloaded the last gromacs CVS version yesterday using

cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login
cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co gmx
cvs update -A -r release-3-3-patches
 I installed it as stated in the website. Then i ran

pdb2gmx -f 1YPC_met59.pdb -water f3c

This is part of the output

Making bonds...
Opening library file
/home/gromacs/LEONARDO/PROGRAMAS/bin/gmx/share/gromacs/top/aminoacids.dat
Number of bonds was 1059, now 1059
Generating angles, dihedrals and pairs...
Before cleaning: 2808 pairs
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3
Source code file: pgutil.c, line: 87

Fatal error:
Atom CB not found in residue 64 while adding improper

-------------------------------------------------------

this are the first and last lines of the pdb i used

ATOM 1 N MET I 20 -11.630 5.328 1.023 0.50 25.84
ATOM 2 CA MET I 20 -10.830 6.245 1.842 0.50 25.77
ATOM 3 C MET I 20 -10.600 7.583 1.122 1.00 25.46
ATOM 4 O MET I 20 -9.908 7.695 0.096 1.00 25.91
ATOM 5 CB MET I 20 -9.516 5.597 2.269 0.50 26.26
ATOM 6 CG MET I 20 -8.596 6.493 3.054 0.50 26.61
ATOM 7 SD MET I 20 -7.353 5.480 3.921 0.50 27.29
ATOM 8 CE MET I 20 -5.854 6.438 3.687 0.50 26.26
ATOM 9 N LYS I 21 -11.225 8.577 1.736 1.00 24.80
(...)
ATOM 497 O VAL I 82 -1.544 11.982 3.001 1.00 8.33
ATOM 498 CB VAL I 82 -4.034 10.892 4.520 1.00 8.78
ATOM 499 CG1 VAL I 82 -3.354 9.761 5.292 1.00 8.61
ATOM 500 CG2 VAL I 82 -5.509 11.010 4.891 1.00 9.72
ATOM 501 N GLY I 83 -0.912 11.916 5.215 1.00 8.31
ATOM 502 CA GLY I 83 0.505 11.680 4.861 1.00 8.56
ATOM 503 C GLY I 83 1.524 12.137 5.881 1.00 8.72
ATOM 504 O GLY I 83 1.121 13.002 6.681 1.00 8.53
ATOM 505 OXT GLY I 83 2.661 11.622 5.866 1.00 9.59
TER 506 GLY I 83


I am not sure if this is a bug; the residue 64(83) is a glycine, so I dont
understand why it complains about CB atoms. When using opls pdb2gmx doesn't
complain at all.

leonardo
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051028/0bc46a81/attachment.html>