[gmx-users] [Fwd: Regarding pair interactions in ligand itp file]

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 2 18:50:48 CET 2006

-------- Original Message --------
Subject: Regarding pair interactions in ligand itp file
Date: Thu, 02 Feb 2006 22:52:03 +0530
From: 4tejender <4tejender at indiatimes.com>
Reply-To: 4tejender <4tejender at indiatimes.com>
To: <spoel at xray.bmc.uu.se>

dear sir,
   can you please tell me more about pair interaction that to included 
in the itp file. which atoms should be included under it and which 
should not. i read the gromacs manual but didn't get much info what it 
actually mean. i read that it is generally 1-4 interactions. but there 
may be some atoms which are in very close vicinity which are not bonded 
directly ie more than 4 bonds away.
   one more thing i want to know it that is the only energetically 
favourable interaction should be included or we have to include all.

with regards
university of hydrabad
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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