AMBER Archive (2008)

Subject: AMBER: ACPYPI announcement

From: Alan (alanwilter_at_gmail.com)
Date: Thu Jul 31 2008 - 06:17:02 CDT

Hi List!

Well, it's a modest contribution and not properly released but I guess
people may find it useful. So 'svn update' and check the website:

http://code.google.com/p/acpypi/

often for any eventual update.

It's ACPYPI, a tool based on Python to use Antechamber to generate
topologies for chemical compounds and to interface with others python
applications like CCPN or ARIA.

acpypi is pronounced as "ace + pipe".

Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM
and AMBER (of course)

NOTE: any topology and parameter files created by antechamber/acpypi
(based on General Amber Force Field - GAFF) is intended to work with
AMBER force fields only. Although I have seen people using ligand in
GAFF and protein in CHARMM force field with apparently good results
for docking, it would be interesting to investigate how a ligand in
GAFF would work with a protein in OPLS/AA force field.

Cheers,
Alan 

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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