Re: [AMBER] help in make .prepin file

From: David A Case <>
Date: Fri, 3 Jul 2015 08:22:16 -0400

On Fri, Jul 03, 2015, Robin Jain wrote:

> I want to create e prepin file for Potassium cation.

First, Amber already has K+ files specially calculated for various water
models. See the "Ions" section in the Amber Reference Manual.

Second, if you really do want to create your own, see the atomic_ions.cmd
file in $AMBERHOME/dat/leap/lib. This shows how the Amber libraries were
created in the first place.

> For this i use
> following procedure- First i make a neutral pdb in Gaussian and then
> convert it into .com file using Antechamber as follows-
> antechamber -i K.pdb -fi pdb -o -fo gcrt -gv 1 -ge K.resp -nc 1
> Then i load this .com file in G09 and calculate job but i got error.

Third, this doesn't make much sense: in a simple force field, the charge on K+
is +1. There is no need to try to calculate RESP charges.

Fourth, saying "i got error" is not a statement that (in general) will
generate much useful help. Providing the exact error message is much more
likely to elicit a helpful response.

...hope this helps...dac

AMBER mailing list
Received on Fri Jul 03 2015 - 05:30:02 PDT
Custom Search