VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Feb 26 2010 - 22:34:42 CST

What about it fails? VMD's routine for recognizing H-bonds is not dependent
on any particular force field.

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Irene Newhouse
Sent: Friday, February 26, 2010 2:40 PM
To: vmd list
Subject: vmd-l: Hbonds calc with residue not in CHARMm

 

We've got a Desmond trajectory that contains a residue not typed in CHARMm -
we used Desmond in the first place because its atoms are typed in OPLS, so
initial setup was much easier. Now we're hoist on that petard, because we'd
like to do an H-bond analysis that includes the untyped residue, and the
procedure fails. Can you recommend a fix? Or do we have to wait until the
Desmond GUI gets upgraded?
 
Thanks!
Irene Newhouse

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