[gmx-users] Packages for building topologies

Justin A. Lemkul jalemkul at vt.edu
Wed May 27 13:33:42 CEST 2009

vivek sharma wrote:
> Hi All,
> I was doing some MD simulation over the docked complex and following the 
> drug-enzyme tutorial for the same. The tutorial provided by Kerrigan's 
> is really helpful. Only problem with the tutorial is generating 
> topologies, for which PRODRG server is suggested. I want to use some 
> stand alone package for generating the topologies which can run on local 
> machine.
> Does anybody have idea of such packages ?

There are several within the Users Contributions section of the website, but 
then you are generally limited to whatever force field the authors of those 
programs decided to use.

If you want a standalone copy of PRODRG, you can request one by clicking "How to 
obtain" at the top of the PRODRG site.


> Suggest me any other alternate of generating topologies.
> With thanks in advance..
> ~Vivek
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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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