[gmx-users] PRODRG again

[Daan van Aalten]

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considered rather outdated even by the Gromacs crew themselves.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