Re: AMBER: problem with prep file generation

From: Junmei Wang <>
Date: Wed, 13 Aug 2008 11:59:49 -0500

Hi, Aneesh
One cannot generate prepi or prepc using prepgen for two different
molecules. But you can generate prepi/prepc for one molecule using multiple
conformations. There is two ways to do this: using individual antechamber
programs (respgen, espgen to get esp from multiple conformations, and
prepgen), or use the latest version of residuegen. We designed residuegen
mainly to generate amino-acid-like or nucleic-acid-like residues, but it can
also be applied to handle normal organic molecules with multiple
conformations. By the way, if you only use one conformation (i.e. one
gaussian output), antechamber should be used for simplicity.

Attached is the latest residuegen.c and a sample input file.



On Wed, Aug 13, 2008 at 7:05 AM, aneesh cna <> wrote:

> Dear Amber Users,
> I am facing a problem with generating prep file. My system contains two
> separate molecule (say X and Y). When I am making a prep file separately for
> each molecule ,it went fine ( Here I am using two different gaussian outputs
> i.e.,X.log and Y.log). But when I am trying to generate a prep file for two
> molecule together ( considering X and Y together as a single molecule)
> using gaussian output XY.log , prep file contain information about only one
> molecule and NEW.PDB also contain coordinates of this molecule (not the
> other molecue,say Y). Why its not considering the second molecule even
> though I used the option '-j 5' ( i used this option because it showed the
> error ' For atom[1] the best APS is not zero, exit' )?. Is there anyway to
> generate a prep these two molecule together?
> Thanks in advance
> Aneesh

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Received on Sun Aug 17 2008 - 06:07:12 PDT
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