[gmx-users] Topology from semiempiricaly optimized structure

[David]

On Sat, 2004-06-12 at 15:43, Semen Esilevsky wrote:
> You see, I've tried PRODRG and it does not work for
> me. It disrupts the geometry I supply even if I don't
> ask for energy minimization. I'm not sure if it is a
> bug, but this server doesn't help much.
That sounds like an exaggeration: the shitty part of it all is to write
down the connectivity. I'm pretty sure PRODRG will get that right. The
next step, creation of the force field, is always your responsibility,
whether or not PRODRG gives you a good starting set. You can use the itp
file from prodrg and then modify whatever you like, if there are clear
errors it most likely is because your molecule is not well described by
the force field in the first place. 



> 
> --- Daan van Aalten <vdava at davapc1.bioch.dundee.ac.uk>
> wrote:
> > 
> > if you are happy with sticking with the ffgmx force
> > field, the PRODRG
> > server will give you a topology for your molecule,
> > see
> > http://davapc1.bioch.dundee.ac.uk/prodrg
> > 
> > Daan
> > 
> > On Fri, 11 Jun 2004, Semen Esilevsky wrote:
> > 
> > > Hi all!
> > > I have a small molecule (a fluorescent probe),
> > which
> > > is optimized on the semiempirical level, so I know
> > the
> > > geometry. As far as I understand the only way to
> > make
> > > a topology for it is to write it by hands using
> > > appropriate atom types and forcefield parameters.
> > > However it seems to be a week of work for ~80
> > atoms.
> > > Does the program (or script) exists for this
> > routine
> > > task?
> > >
> > > Thank you in advance,
> > > Semen
> > >
> > >
> > >
> > >
> > >
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> > 
> >
> ##############################################################################
> > Dr. Daan van Aalten                    Wellcome
> > Trust Senior Fellow / Reader
> > Wellcome Trust Biocentre, Dow Street   TEL: ++ 44
> > 1382 344979
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> > 
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> 
> 
> 	
> 		
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 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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