[gmx-users] Updated topology generation tool available

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 11 22:09:36 CEST 2009

Hi All,

I have added uploaded a new version of TopolGen, version 1.1, to the Users' 
Contributions section of the website.  This program is written in Perl and is 
designed to generate a topology for use with the OPLS-AA force field from an 
all-atom PDB file.

Based on input from many users of the past few months, I think I have made some 
real improvements.  Most notable among these are primitive atom typing and 
charge assignment.  As always, the user is cautioned to check the topology and 
validate these parameters.  It is impossible to test all combinations of 
parameters and validate them, so it is up to you to do so!  Please consult the 
README for all the new changes.

Please feel free to contact me on this list or privately if you have questions, 
comments, suggestions, or you find a bug.




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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