[gmx-users] Problem in Disulfide Bond between different chain!
Mark.Abraham at anu.edu.au
Wed Jan 11 12:16:44 CET 2012
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.
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