From: Irene Newhouse (
Date: Thu Mar 04 2010 - 12:52:08 CST

H-bonds worked just fine with the pdb file written from one frame of the Desmond trajectory. So I did this:


-loaded that pdb file into VMD

-loaded the Desmond .cms file into the same molecule

-loaded the Desmond trajectory into the same molecule


Now H-bonds works just fine!!


Thanks a lot for your help!


Subject: Re: vmd-l: Hbonds calc with residue not in CHARMm
Date: Wed, 3 Mar 2010 16:05:28 -0600

I vaguely recall seeing something like this before with problematic molecule names (maybe because they had spaces? I'm not sure now). Can you try this:

-Start VMD 1.8.7 fresh
-load the PDB you sent me
-start the Hydrogen Bonds plugin from the menu
-run it with some input and "unique hbond" selected for detailed info

The graph will be empty (only one frame) but you should see the details in the tkconsole (and no error in the VMD console).

Let me know how this behaves.


On Mar 3, 2010, at 3:50 PM, Irene Newhouse wrote:

It's pretty much the same thing. Selection 1 is left at protein, sel 2 is set either to resname ACT or resid 134 [both of which apply]. I vi-ed the .cms file; resname ACT *is* in there.
The Application Error window says Error: list element in braces followed by "." inst...
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