[gmx-users] charges

[Luciane Vieira de Mello]

Dear David,

thank you very much for your help.
But, I have already tried to use prodrg, the problem is the program
assumes the molecule is uncharged, what is not true - it's 3-.
Any other clue??

thanks




On 18 Oct 2002, David van der Spoel wrote:

> On Fri, 2002-10-18 at 12:57, Luciane Vieira de Mello wrote:
> >
> > Hello,
> >
> > I want to run a MD for a protein and its ligand. However, the ligand
> > topology is not available on gromacs.
> >  So, I would like to know the easiest way to calculate atomic charges for
> > small molecules?
> the easiest way to get charges is using the prodrg server which uses
> charges by analogy. There is no easy way however, and no standard recipe
> like Amber has.
>
> >
> > thanks
> >
> >
> > +-------------------------------------------------------------------------+
> > |                  Dra. Luciane Vieira de Mello Rigden                    |
> > | e-mail: mello at cenargen.embrapa.br                                       |
> > | Embrapa Recursos Geneticos e Biotecnologia                              |
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> > +-------------------------------------------------------------------------+
> >
> >
> >
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 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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