RE: AMBER: (no subject)

From: FyD <>
Date: Wed, 14 Jul 2004 21:30:04 +0200


> I am going through the plastocynin tutorial. Can you tell me
> how I can use
> GAFF of antechamber for this purpose, since i could not
> figure out how to
> use the resp charges generated by RED as there is no relevent
> file type which can be used.

R.E.D. generates a Tripos "Mol_o.mol2" file with the RESP/ESP charges in it.

To load this file into leap/amber8 (only), run:
xleap -f leaprc.ff99

M = loadmol2 Mol_o.mol2
saveamberparm M M.crd

Before be sure to manually add the atom types needed according to the Cornell
al. paper, (JACS 117 5179. See Table 1 "List of atom types"), i.e. modify the
6th column of this .mol2 file:
Personnally, I prefer to "manually" add the atom types because this step is
crucial and determines your FF accuracy. As said Ross, you have to be aware of
what you do...

Using "saveamberparm M M.crd" leap (1st run), it is going to tell you,
which FF params are missing. Then, you can create your personnal FRCMOD file
(using GAFF or by fitting ab-initio data) which contains 'your' NEW FF params
that can be load into leap (in a 2nd run) i.e. using:
xleap -f leaprc.ff99

M = loadmol2 Mol_o.mol2
FRCMOD = loadamberparam frcmod.Anshul
saveamberparm M M.crd

Regards, Francois
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Received on Wed Jul 14 2004 - 20:53:00 PDT
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