[gmx-users] pdb2gmx: S-S bond

Mateusz Nowak mynowak at cyf-kr.edu.pl
Sun Jul 7 18:42:11 CEST 2002


I have produced topology file for protein with pdb2gmx v. 3.0, using
Gromos96 43a1 forcefield. There are some disulfide bonds there, but when I
look at top file, there are not bond type codes assigned to S-S atom pairs
in [ bonds ], although the pairs themselves are specified there. Is this
ok, if [ bonds ] for S-S remains empty?
I can see in ffG43a1bon.itp file that this bond should be of gb_33 type.
Should I fill this manually in top file?

Thanks in advance.

Mateusz Nowak

More information about the gromacs.org_gmx-users mailing list