[gmx-users] New topology generation tool available

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 3 12:49:29 CEST 2009

Hi All,

I have added a new program to the Users' Contributions section of the website. 
TopolGen is yet another topology-building tool that will produce a rough 
OPLS-AA-compatible topology from an all-atom PDB file.  Please refer to the 
README included with the program (written in Perl) for specific implementation 
details.  The main advantage to the script is that it makes use of the CONECT 
records in the PDB file to determine all bonded parameters.

The caveat is that TopolGen thus far makes no effort to assign atom types and 
charges.  This is an area of further development, but is not much more work for 
the user than the modifications that one often makes to e.g. PRODRG-generated 

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
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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