<div>Hi everone.</div> <div>I'm studying on a protein including two chains with <STRONG>four</STRONG> disulfide bonds.when I<BR>watched the simulation I saw that A and B chains were splitting from<BR>eachother.Then I gave that command.<BR> pdb2gmx -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge -ss -inter -ignh.</div> <div>But the chains split from eachother again.In specbond.dat only one CYS-CYS bond appears.Should I add three more lines to the file like this?</div> <div>CYS SG 1 CYS SG 1 0.2 CYS2 CYS2<BR></div> <div> </div> <div>What can I do to identify the -SS bond other than these?</div> <div> </div> <div>Thank you</div> <div>Best regards</div> <div>Fulya Caglar</div> <div>Hacettepe University</div><p> 
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