[gmx-users] Problem in Disulfide Bond between different chain!

Xianwei Wang wangxianwei1228 at 163.com
Wed Jan 11 12:00:55 CET 2012

 Dear all:
I want to do  a simulation using a dimer, but the system is connected by 2 disulfide bonds between A-chain and B-chain. I have produced topology file for protein with pdb2gmx using AMBER99SB forcefield. In order to bond disulfide bonds I using flag -ss. If I do not delete the TER line between A-chain and B-chain in .pdb file, the program pdb2gmx can not recognize the disulfide bonds between A-chain and B-chain. But if I delete the TER line, I get the two bonds successfully. There  would be another problem, the C-terminal of A-chain and the N-terminal will be bonded in the .top file. How should I do?
I am using gromacs 4.5.4!

Sincerely yours,
Xianwei Wang

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120111/28ec100c/attachment.html>

More information about the gromacs.org_gmx-users mailing list