VMD-L Mailing List

From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Wed Aug 24 2011 - 10:08:41 CDT

Hi John,

Thanks a lot for your reply. Does this plugin also work for lipid system or only works for protein and DNA?

Emilia

On Aug 23, 2011, at 5:05 PM, John Stone wrote:

>
> Hi,
> If you want to use the new Chirality plugin in VMD 1.9, you must
> first issue the command "package require chirality"
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Aug 23, 2011 at 04:13:53PM -0500, Ling Wu wrote:
>> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078