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

[David van der Spoel]

On Fri, 2004-01-09 at 11:06, saurabh shakya wrote:
> Hello ,
> I am trying a mdrun on a system in which cystines are
> bound to
> Fe of iron sulfur cluster .I have calculated the
> charges on the iron sulfur
> cluster  and the 4 cystines ,the charges on cystine
> are as follows 
>     6 N           -0.4821
>     7 H            0.218549
>     8 Ca            0.702265
>     9 Ha          -0.071973
>    10 Cb           -0.276902
>    11 Hb           0.196618
>    12 Hb            0.062929
>    13 Sg           0.006376
>    14 C           0.200239
>    15 O          -0.275707
> 
> Now when i am trying to use these charges in the force
> field (oplsaa) i am running into lincs warning
> for the different atoms of cystine like Cb-Hb ,Cb-Ca
> .Is it ok to alter the charges in the forcefield ? if
> not how can i account for the changed charges due to
> binding with Fe?

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?

> Thanks
> 
> Regards
> Saurabh
> 
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-- 
David.
________________________________________________________________________
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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