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

David Mobley dmobley at gmail.com
Fri Feb 16 16:20:51 CET 2007


> How does one build a topology using a different force field (say for
> instance, oplsaa)?  Is there a simple way to do it,

I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS that automatically generates
parameters. Of course, this is not the same as a topology.

Another option is using the Antechamber package. If you have AMBER, I
have a conversion script you can use that will convert Antechamber's
AMBER topologies and coordinates into GROMACS topologies and
coordinates. This is pretty much a fully automatic process, so it is
fairly painless.


> Thanks,
> Arneh
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