[gmx-users] charges

[David van der Spoel]

On Fri, 2002-10-18 at 13:27, Luciane Vieira de Mello wrote:
> 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??

try assigning charges by analogy with proteins, e.g. for a carboxylic
group you use the charges on an ASP sidechain.
If that doesn't work the you should look into doing quantum chemistry
calculations.

> 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                              |
> > > | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> > > | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> > > | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> > > +-------------------------------------------------------------------------+
> > >
> > >
> > >
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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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-- 
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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