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

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Sat Feb 17 05:01:34 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.


Hi, David,

That is very good. Could you send it to me or put it online so that
every one can download it?


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