Thanks alot Marc.....
I have one query regrading these parameters:Aren't these parameters
specific for Amber94 forcefield?
Actually, I would be using Amber03 forcefield for the
simulations......Would these parameters work for ff03 forcefield too?
Thanks again.
Neeru
On Sat, Dec 10, 2011 at 4:40 PM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Sorry, should be www.pharmacy.Manchester.ac.uk/bryce/Amber
>
> On Saturday, 10 December 2011, Marc van der Kamp <marcvanderkamp.gmail.com
> >
> wrote:
> > Hi neeru,
> > You can find parameters/topology (+ reference) at
> www.bryce.pharmacy.Manchester.ac.uk/bryce/Amber
> >
> > Marc
> >
> > On Saturday, 10 December 2011, neeru sharma <neeru.bioinfo.gmail.com>
> wrote:
> >> Dear amber users,
> >>
> >> I have to simulate a protein-GDP complex. For this,I have generated
> Amber
> >> topology and coordinate files for GDP molecule after preparing GDP.lib
> and
> >> frcmod.GDP.
> >>
> >> But the topology and co-ordinates file are quite different from the
> input
> >> PDB file and hence the parameters are also faulty, the GDP molecule is
> not
> >> fitting in the binding pocket of protein (Upon superimposition of the
> >> generated topology and coordinate file with the initial PDB input file,
> >> they were not being superimposed).
> >>
> >> Upon tracking the whole process, it was found that the error might be
> while
> >> using antechamber for generating prepin file using Gaussian output file
> as
> >> the input.
> >>
> >> Can anyone please suggest some way to apply some constraints in the
> >> antechamber command itself. OR if anybody has the paramters or topology
> for
> >> GDP, can anyone provide me the same so that I can compare and see where
> the
> >> parameters are differing.
> >>
> >> Thanks
> >>
> >> ----
> >> Neeru Sharma
> >> Pune (India)
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Neeru Sharma
Project Engineer,
Molecular Modelling Team, Bioinformatics Group,
Centre for Development of Advanced Computing (CDAC),
Ganeshkhind, Pune University Campus,
Pune, Maharashtra - 411007
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Received on Sat Dec 10 2011 - 06:00:02 PST
