From: AHMET BAKAN (ABAKAN_at_KU.EDU.TR)
Date: Fri Jun 04 2004 - 15:01:04 CDT
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 http://home.ku.edu.tr/~abakan
It may be unintelligible, since I wrote it after my first couple of topology definitions. Tell me if I can help more.
From: Marek Dynowski <marek.dynowski_at_student.uni-tuebingen.de>
Date: Fri, 4 Jun 2004 17:53:27 +0200
Subject: namd-l: Simulation with ammonia
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 ------------------------ ==============ABC============== Ahmet BAKAN Chemistry, Junior Koc University abakan_at_ku.edu.tr MSN ahmetbakan_at_msn.com ICQ #86167698 http://home.ku.edu.tr/~abakan
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