[gmx-users] [Fwd: charge groups - short question]

[David]

-----Forwarded Message-----

From: Dr. Csaba Hetenyi <csabahete at yahoo.com>
To: David <spoel at xray.bmc.uu.se>
Subject: charge groups - short question
Date: 02 Mar 2003 05:53:46 -0800

Hej David, 

I am performing GROMACS simulations for drug-protein
systems and will make LIE at the end.
The program works well, for 3500 atoms a 2ns dynamics
takes 10 days on the PIV with that GHz...:)
---
My ligand has some non-aminoacid parts. First, i just
made it with the prodrug server, and let it give 0
charge for some non-AA atoms. Now, i am thinking about
using a standard charge system for the ligands (eg.
Gasteiger) as my other ligands have larger non-AA
parts and i need to precisely compare them (the dGs)
later.
However, Gasteiger (and also other charge calculator
possibilities) does not know anything about charge
groups. I am wondering, if the whole ligand could be
used as one charge group, as there is no hope to make
integer charges for only some groups of ligands. Or i
can just define some atoms for a group even if the
total charge is only close to an integer?
Have you had such a problem before?
I think, this problem could occur for other guys
interested in some drug problems, as drugs are usually
not consisted of AAs.
---
Otherwise, i realised that the best thing in GROMACS
is the indexing (from a practical point of view). This
is a great help for the user...
Best wishes,
Csaba

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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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