VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Sat Feb 27 2010 - 11:33:43 CST

The VMD console window says that no bonds are found - even when I do protein-only selections. The error message window comes up. When I look at the details, it's very complicated. We loaded the .cms file & clickme.whatever.

 

Thanks!

Irene
 

From: gumbart_at_ks.uiuc.edu
To: einew_at_hotmail.com; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Hbonds calc with residue not in CHARMm
Date: Fri, 26 Feb 2010 22:34:42 -0600

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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