Thanks for your help, David. Have gotten it to work now.
On a similar note, has anyone had success modeling GCP
(or phosphomethylphosphonic acid guanylate ester
)? It is the nonhydrolizable analogue of GTP - replace the oxygen bridging
the phosphate groups with a carbon.
Structure can be found
http://xray.bmc.uu.se/hicup/GCP/index.html
What approach would you suggest, as those parameters are not available
(although those for GTP are)?
Thanks,
Brandon
On Tue, Jun 19, 2012 at 4:24 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Jun 18, 2012, Brandon Sim wrote:
> >
> > This is incorrect: the GDP files at the website above should have
> everything
> > > you need.
> > >
> >
> > There is an .frcmod file there - could you or anyone else outline briefly
> > how to use just the parameter file to create a unit to load to create a
> > library file such that minimisation can occur?
>
> There is a "guide to usage", a frcmod file and a prep file. After reading
> the
> "guide to usage", you basically use loadAmberPrep to load the prep file,
> loadAmberParams to load the frcmod file, and loadPdb to load a pdb file.
> If
> you have other components (e.g. a protein) you would also need to source an
> appropriate leaprc file, such as leaprc.ff12SB.
>
> ...good luck....dac
>
>
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Received on Tue Jun 19 2012 - 22:30:03 PDT
