[gmx-users] Building Topology of a Drug (using the ff of your choice)

Mitchell J Stanton-Cook s4026869 at student.uq.edu.au
Fri Feb 16 03:37:28 CET 2007


   You could use PRODRG to build an initial topology and then use the FF
definition in you gromacs distribution to edit to suit.

On the PRODRG website, there is a link to the top right had of the page
if memory serves me correctly to a beta server that will generate
topology files consistent with the 43a1 FF.

Cheers Mitch

On Thu, 2007-02-15 at 17:48 -0800, Arneh Babakhani wrote:
> Hi , I'd like to build a topology of a Drug.  I'm aware of the PRODRG 
> website. 
> But if my understanding is correct, on this website, you can only build 
> using one forcefield (GROMOS87). 
> How does one build a topology using a different force field (say for 
> instance, oplsaa)?  Is there a simple way to do it,
> Thanks,
> Arneh
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