Re: AMBER: building new ions

From: FyD <>
Date: Mon, 15 Dec 2008 15:09:04 +0100

Hi Fatima,

> I am looking at ways to build an organic salt : Choline Chloride
> C5H14ONCl. Cl- is already built in Amber
> I need to build C5H14N+
> any hints on how i can do this

You need to develop a new force field library for C5H14N+ with RESP
charge values. The R.E.D. tools can be used for that. Below is a short

1) Prepare inputs
pdb file -> .p2n file using Ante_RED (from R.E.D.-III tools)
          -> .com Gaussian input file (using Ante_RED from R.E.D.-III tools)
          -> .inp GAMESS input file

2) run Gaussian from the .com file to generate QM .log file
or run GAMESS from the .inp file to generate QM .log file

3) run R.E.D. from the .log + .p2n files to get a .mol2 file
    you might also directly use R.E.D. from step 1) - using only the
P2N file as input.

4) load the .mol2 file into LEaP to generate the OFF library
or you can load the .mol2 file directly (as this is a whole molecule &
not a molecule fragment).

Once your P2N file is built, this can be done very quickly using R.E.D.

I hope this helps,

regards, Francois

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Received on Wed Dec 17 2008 - 01:09:45 PST
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