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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