[gmx-users] HELP .....changing charges in the forcefield

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 9 13:19:01 CET 2004

On Fri, 2004-01-09 at 12:30, saurabh shakya wrote:
> there are total 2 irons and 2 sulfurs which are
> covalently bonded as a iron sulfur cluster. these
> irons in turn are bonded to 2 cystines each making a
> total of 4 cystines bound to the 2 irons of the
> cluster. These cystines are covalently bonded to the
> Fe of the cluster  by the Sg . 
> Other thing which puzzles me is that the same topology
> with the default gromacs charges was running fine in
> position restrained and unrestrained md run .But after
> I alter the charges in the same topology ,lincs error
> starts coming in position restrained md .

Weird indeed... As a general rule I would only change the charges on the
side chain, not the backbone though, you can do this in Gaussian by
replacing the Calpha by an extra hydrogen. Furthermore I forgot what
kind of cut-off treatment you have used. For PME it shouldn't matter,
but for cut-off it might make a difference how you define charge groups.

To do this correctly, you would have to define a new reside FE2S2 (with
internal geometry, i.e. bonds, angles), and define special bonds between
all  Fe and Cys.
> Regards 
> Saurabh
> there is not a real problem with modifying charges, I
> suspect there is
> still something else in the topology. How are the
> cysteines connected 
> to
> the Iron-Sulfur cluster? How many Iron and Sulfur and
> Cysteines do you
> have?
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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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