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

[Mark Abraham]

On 11/01/2012 10:11 PM, Xianwei Wang 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!
>

See pdb2gmx -h about -chainsep. With suitable choice of -chainsep, TER 
and chain IDs this problem can be solved.

Mark
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