VMD-L Mailing List
From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Tue Aug 23 2011 - 16:13:53 CDT
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Hi All,
I want to use extrabonds command to restrain some dihedral angles in my lipid system, so I can have the correct chirality and Cis-trans isomerism through MD simulation. I noticed that VMD can generate corresponding extrabonds.txt file, but It did not work for me, I tried chirality restrain -o chirality-extrabonds.txt in VMD TkConsole, it gave me this message "invalid command name "chirality"". Since my system has a lot of lipids, so I am trying to avoid writing those atom numbers by myself. Does anyone have any experience about this?
Thanks in advance!
Emilia
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