VMD-L Mailing List
From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Feb 27 2010 - 12:05:18 CST
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VMD's built-in macros like "protein" wouldn't include non-standard residues,
so that could be part of the problem. If you want to send me your files
off-list, I can figure out what's going on.
From: Irene Newhouse [mailto:einew_at_hotmail.com]
Sent: Saturday, February 27, 2010 11:34 AM
To: gumbart_at_ks.uiuc.edu; vmd list
Subject: RE: vmd-l: Hbonds calc with residue not in CHARMm
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
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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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