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

[Vitaly Chaban]

>
> 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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