[gmx-users] charges

[Daan Virtual]

Dear Lucy

The solution to your problem is quite simple : at the bottom of the PRODRG
page there is a row of buttons - one of them is "Full Charges" - this is
set by default to NO.  If you set it to yes you will get a charge of -1 on
the carboxylate and -1 on the phosphate. I am aware the latter is not
correct in this context but similar parameters were used for the phosphate
backbone for DNA in GROMOS '87 simulations. If you want the -PO4 to carry
a -2 charge you could as an approximation multiply all the partial charges
(in PO4 ONLY) by 2.

Hope this helps

Daan

On Fri, 18 Oct 2002, 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??
>
> 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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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O