Re: Simulation with ammonia

Date: Fri Jun 04 2004 - 15:01:04 CDT

Hi Marek,

The solution seem to be preparing your own topology file manually, I have prepared many for drug molecules and monomers.
I have prepared a recipe which is available on
It may be unintelligible, since I wrote it after my first couple of topology definitions. Tell me if I can help more.


-----Original Message-----
From: Marek Dynowski <>
Date: Fri, 4 Jun 2004 17:53:27 +0200
Subject: namd-l: Simulation with ammonia

Dear all,

I've tried to make a simulation with ammonia and used PSFGEN to produce the
PSF file. But now I have the problem, that there is no definition for
ammonia in the CHARMM Topology File. I would like to now if there is a
solution to produce this entry without using programs like X-Plor or if there
is a CHARMM Topology File for download which contains entries for ammonia.
Thanks for all, Marek.

Marek Dynowski
ZMBP, Plant Physiology
University of Tuebingen
Auf der Morgenstelle 1
D-72076 Tübingen
Ph: +49 7071 29 74643
Chemistry, Junior
Koc University
ICQ #86167698

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