VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Aug 28 2006 - 00:56:18 CDT

Can you tell us exactly how you are doing it in the tkcon? I don't think
you should need to do this, but you could type

 

regenerate angles dihedrals

 

at the end of your psfgen session and see if that fixes your problem.

 

  _____

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Thomas Caulfield
Sent: Friday, August 25, 2006 3:59 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: removing structures from a psf&pdb

 

Hello All:

 

Does anyone have a handy script that can remove a particular molecule from a
psf & pdb and resave the psf and pdb? I tried using tkCON, but it only made
a list of the bonds, and skipped the angels, dihedrals, etc.

 

Thanks,

 

-Tom

 

****************************************

Tom Caulfield, Ph.D. Candidate

School of Chemistry & Biochemistry

Cherry Emerson Bldg., RM 329

Georgia Institute

of Technology

Atlanta, GA 30332-0400

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