[gmx-users] Re: acetonitrile from amber to gromacs

Vitaly Chaban vvchaban at gmail.com
Wed May 19 19:29:13 CEST 2010

> hi all together,
> this week i'm trying to do some simulations with acetonitrile (AN) as a
> solvent and using ffamber99 as force field. on this website
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
> i found a gorgeous little box containing a pretty number of 6-site
> modeled AN molecules, represented by 3 files:
> ch3cn_210.pdb
> frcmod.ch3cn
> prep.ch3cn
> does anyone have an idea, how to generate .gro/.itp files out of these
> amber files, preferably by pushing a single button of some proper tool??
> i'ld be the happiest guy in world if someone told me the trick!
To traslate PDB into GRO, use editconf (gromacs utility).
To get ITP, use X2TOP (gromacs utility).

Also see the topology archive on the gromacs website. A few years ago I
uploaded some working examples with ACN.

Dr. Vitaly Chaban
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