[gmx-users] PRODRG again

[Alan Wilter Sousa da Silva]

Hi Daan,

I'm not a gromos96 expert but if I can download your PRODRG, could I
change your database to start including Gromos96 FF?

I do not promiss anything...  Just wondering.

Cheers,
--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
São José dos Campos (SP), Brasil
www.lac.inpe.br/~alan

On Thu, 20 May 2004, Daan van Aalten wrote:

>
> Hi Osmany
>
> Send us your coordinates/input and we'll return you the topology - or get
> a local copy of PRODRG (see FAQ)
>
> Daan
>
>
> On Wed, 19 May 2004, Osmany Guirola Cruz wrote:
>
> > I have a "drug" greater than 300 atoms what should I do to get the
> > topology
> > I don know if exist another program or server that do something similar
> > My drug have 310 atoms
> > Help please  :-(
> >
> >
> >
> >
> > -----Original Message-----
> > From: Daan van Aalten [mailto:vdava at davapc1.bioch.dundee.ac.uk]
> > Sent: Wednesday, May 19, 2004 9:58 AM
> > To: Peter Zoon
> > Cc: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] PRODRG
> >
> >
> >
> > Peter
> >
> > You are confusing topology with conformation. For each bond between a
> > pair of atoms there is a choice of several hundreds of bond types, which
> > are associated with a) specific force constants and b) specific
> > equilibrium values (i.e. bond lengths). Same for bond angles. You can
> > minimize coordinates, but the topology stays the same.
> >
> > Writing out a G96 FF topology is probably only a day's work if I can
> > have a full day's use of a G96 FF guru for advice and testing - and of
> > course everyone is busy!
> >
> > cheers
> >
> > Daan
> >
> > On Wed, 19 May 2004, Peter Zoon wrote:
> >
> > > >The atom types aren't the problem but the manual conversion of
> > > >bonds/angles/dihedrals to G96 types. IMHO this may be intricate in
> > > >some cases. I guess it would be very nice to have a G96 topology
> > > >automatically generated by PRODRG, the GMX force field seems to be
> > > >considered rather outdated even by the Gromacs crew themselves.
> > >
> > > That doesn't matter right?
> > > If you do a minimization (after you changed to the right atom-types),
> > > the system will just equilibrate and you will reach the right topology
> >
> > > automatically.
> > >
> > > Or am I making a reasoning error here?
> > >
> > > Peter
> > > _______________________________________________
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> >
> >
> > ########################################################################
> > ######
> > Dr. Daan van Aalten                    Wellcome Trust RCD Fellow /
> > Reader
> > 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: see WWW page
> > Univ. of Dundee, Dundee DD1 5EH, UK    WWW:
> > http://davapc1.bioch.dundee.ac.uk
> >
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>
>
> ##############################################################################
> Dr. Daan van Aalten                    Wellcome Trust RCD Fellow / Reader
> 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: see WWW page
> Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk
>
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