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

Suman Nandy nandy.suman at
Wed Jan 11 12:40:59 CET 2012

use -chainsep interactive option in pdb2gmx.


On Wed, 11 Jan 2012 16:42:12 +0530  wrote
>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


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Suman Kumar Nandy
Senior Research Fellow
Department of Biochemistry & Biophysics
University of Kalyani
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