Dear Mr Suman:<br>Thank you very much for your help !<br>Sincerely yours <br>Xianwei Wang<br><br>At 2012-01-11 19:42:24,"Suman Nandy" <nandy.suman@rediffmail.com> wrote:<br> <blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>
use -chainsep interactive option in pdb2gmx.<br>
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Suman<br>
<br>
On Wed, 11 Jan 2012 16:42:12 +0530 wrote<br>
>Dear all:<br>
I want to do a simulation using a dimer, but the system is connected by 2<br>
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>
Sincerely yours,<br>
Xianwei Wang<br>
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<br><br>Suman Kumar Nandy<br>
Senior Research Fellow<br>
Department of Biochemistry & Biophysics<br>
University of Kalyani<br>
Kalyani-741235<br>
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