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On 11/01/2012 10:11 PM, Xianwei Wang wrote:
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all:<br>
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? <br>
I am using gromacs 4.5.4!<br>
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See pdb2gmx -h about -chainsep. With suitable choice of -chainsep,
TER and chain IDs this problem can be solved.<br>
<br>
Mark<br>
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