[gmx-users] Re: Too close water molecules

David spoel at xray.bmc.uu.se
Tue Jan 6 11:50:01 CET 2004

On Tue, 2004-01-06 at 11:22, saurabh shakya wrote:
> 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.

Normally pdb2gmx should make the bond between Cys and Fe automatically,
and there are quite a few extra interactions involved

How come you have done it manually?

If your iron is not in a heme environment you may need to add lines to
the file share/top/specbond.dat, like (for bondlength of 0.2 nm):

CYS     SG      1       FE     FE      1       0.2     CYS2    FE

> The resulting topology runs fine without water but not
> in water so i suspect there is something wrong other
> than the topology.
> Regards
> Saurabh
> 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 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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