[gmx-users] Re: Too close water molecules

saurabh shakya shakya_79 at yahoo.com
Tue Jan 6 11:23:01 CET 2004

The atoms getting close are OW-cys-Hb and the lincs
warning almost always occur for Hb .
I have a Fe attached to the Sg in my system so I have
explicitly specified the improper dihedral between
Hb-Cb-Sg-Fe and all the other bonds,angles and pairs
,while removing all these parmeters for the Hg as
pdb2gmx automatically generates Hg and generates all
these values.
The resulting topology runs fine without water but not
in water so i suspect there is something wrong other
than the topology.


Date: Mon, 5 Jan 2004 19:26:10 +0100 (CET)
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Re: Too close water molecules
Reply-To: gmx-users at gromacs.org

On Mon, 5 Jan 2004, saurabh shakya wrote:

>I am using the opls force field and the cystines are
>neutral .I have tried spc,flexscp and tip3pgmx type
>water but the problem remains the same.

which atoms are getting close? OW-Cys-Hg? Could you
check whether the 
Cb-Sg torsion has a dihedral attached to it? 

David van der Spoel, PhD, Assist. Prof., Molecular
Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala
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

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