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

[Xianwei Wang]

 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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