VMD-L Mailing List

From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Tue Aug 23 2011 - 16:13:53 CDT

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