VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Feb 27 2010 - 12:19:17 CST

That does sound strange. Can you send me just a single frame from the
trajectory in PDB format?

 

From: Irene Newhouse [mailto:einew_at_hotmail.com]
Sent: Saturday, February 27, 2010 12:17 PM
To: gumbart_at_ks.uiuc.edu; vmd list
Subject: RE: vmd-l: Hbonds calc with residue not in CHARMm

 

I understand that 'protein' excludes the nonstandard residues. When every
attempt I made to compute H-bonds specifying the nonstandard residue first
by resname, then by resid, & finally using the index of one of the atoms
involved in H-bonding failed, I decided to see if I could get ANY H-bonds,
so I made some selections not including the nonstandard residue & was
surprised when those didn't work either -- got very similar-looking errors.
I'm using the hbonds.tcl script you emailed me about a year ago - could be
there's something more recent that does work?
 
How would I pare down the traj to something mailable? It's a huge fileset...

Thanks a lot!
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: Sat, 27 Feb 2010 12:05:18 -0600

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
 

  _____

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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