pdb2gmx does not identify disulphide bridges correctly
It is impossible to set sulphur bridges manually, and the automatic detection does not seem to work.
#1 Updated by David van der Spoel about 12 years ago
Please upload an example and tell us which force field you use. I tried processing BPTI (1ld5, http://www.pdb.org/pdb/explore.do?structureId=1LD5) and it works without problems.
#2 Updated by Erik Lindahl about 12 years ago
This is due to pdb2gmx hardcoding atom names and changing CYSH->CYS. This is quite ugly and should be changed, but to get 4.0 out the door I've just added proper renaming for the Amber force field too, which is the only one that differs at the moment. I'll commit to the 4.0 branch in a second.