Hello!!<br>
<br>
I downloaded the last gromacs CVS version yesterday using <br>
<p class="MsoNormal"><span style="font-size: 8pt; font-family: "Courier New";" lang="EN-GB">cvs -z3 -d :pserver:anoncvs@cvs.gromacs.org:/home/gmx/cvs
login<br>
cvs -z3 -d
:pserver:anoncvs@cvs.gromacs.org:/home/gmx/cvs co gmx</span><span style="font-size: 8pt; font-family: "Courier New";" lang="EN-GB"><br>
cvs update -A -r release-3-3-patches</span>
<br>
</p>
I installed it as stated in the website. Then i ran<br>
<br>
pdb2gmx -f 1YPC_met59.pdb -water f3c<br>
<br>
This is part of the output<br>
<br>Making bonds...<br>
Opening library file /home/gromacs/LEONARDO/PROGRAMAS/bin/gmx/share/gromacs/top/aminoacids.dat<br>
Number of bonds was 1059, now 1059<br>
Generating angles, dihedrals and pairs...<br>
Before cleaning: 2808 pairs<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 3.3<br>
Source code file: pgutil.c, line: 87<br>
<br>
Fatal error:<br>
Atom CB not found in residue 64 while adding improper<br>
<br>
-------------------------------------------------------<br>
<br>
this are the first and last lines of the pdb i used<br>
<br>
ATOM 1 N MET I
20 -11.630 5.328
1.023 0.50 25.84<br>
ATOM 2 CA MET I
20 -10.830 6.245
1.842 0.50 25.77<br>
ATOM 3 C MET I
20 -10.600 7.583
1.122 1.00 25.46<br>
ATOM 4 O MET I
20 -9.908 7.695
0.096 1.00 25.91<br>
ATOM 5 CB MET I
20 -9.516 5.597
2.269 0.50 26.26<br>
ATOM 6 CG MET I
20 -8.596 6.493
3.054 0.50 26.61<br>
ATOM 7 SD MET I
20 -7.353 5.480
3.921 0.50 27.29<br>
ATOM 8 CE MET I
20 -5.854 6.438
3.687 0.50 26.26<br>
ATOM 9 N LYS I
21 -11.225 8.577
1.736 1.00 24.80<br>
(...)<br>
ATOM 497 O VAL I
82 -1.544 11.982
3.001 1.00 8.33<br>
ATOM 498 CB VAL I
82 -4.034 10.892
4.520 1.00 8.78<br>
ATOM 499 CG1 VAL I
82 -3.354 9.761
5.292 1.00 8.61<br>
ATOM 500 CG2 VAL I
82 -5.509 11.010
4.891 1.00 9.72<br>
ATOM 501 N GLY I
83 -0.912 11.916
5.215 1.00 8.31<br>
ATOM 502 CA GLY I
83 0.505 11.680
4.861 1.00 8.56<br>
ATOM 503 C GLY I
83 1.524 12.137
5.881 1.00 8.72<br>
ATOM 504 O GLY I
83 1.121 13.002
6.681 1.00 8.53<br>
ATOM 505 OXT GLY I
83 2.661 11.622
5.866 1.00 9.59<br>
TER 506 GLY I 83<br>
<br>
<br>
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.<br>
<br>
leonardo<br>