[gmx-users] Questions regarding the Vacuum forcefield andHistidinecharges

[Joanne Hanna]

Yes that was the question I was aking, so if you only define one hydrogen to be added (hisa, Hisb) the histidine remains neutral, but if you put both on (hish) then it becomes +1. So if you have no strong preference as to whether they should be neutral or positive then is it best to leave this choice to the default where this decision is based on an optimal hydrogen bonding conformation? or should you define the histidines as hish? any advice!

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com
>>> spronk at its.caltech.edu 05/04/05 17:22 PM >>>
Sorry if I didn't understand you correctly, but to get a
positively-charged His you need to put not just a single hydrogen but two
hydrogens on the ring--one on ND1 and one on NE2.

Steve

On Wed, 4 May 2005, Joanne Hanna wrote:

> Yes I have tried choosing both options that you can have to put a single
> hydrogen on HisA and HisB i think.
>
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
>
> J.F.Hanna at warwick.ac.uk
> jfhanna at gmail.com
> >>> x.periole at rug.nl 05/04/05 15:48 PM >>>
> Joanne Hanna wrote:
>
> >Thanks for your reply
> >
> >Regarding th Histidine question I specified it using -inter, I have also done this without specifing the type of histidines and it still gives the same result.
> >
> >
> >
> Do you get through the dialogue where you got to choose the type of
> histidine ?
> If yes that could be a bug that you should report to the developpers ...
>
> >Also would you know how i could alter the charges in the topologies that i have built myself in order to use these ligands in my vacuum calculation.
> >
> >
> You can alway use the topology that is given by the regular force field,
> which would be the
> equivalent of modifying the topology of the vaccum FF to put back the
> charges.
>
> --
> ----------------------------------
>  Xavier Periole - Ph.D.
>
>  Dept. of Biophysical Chemistry / MD Group
>  Univ. of Groningen
>  Nijenborgh 4
>  9747 AG Groningen
>  The Netherlands
>
>  Tel: +31-503634329
>  Fax: +31-503634800
>  email: x.periole at rug.nl
>  web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
>
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