i suggest using imin=5, using the -y flag to read the trajectory (see the
manual for details).
set igb>0 (exact value doesn't matter if you aren't interested in solv
energy), gbsa=2 and surften=1, and the Esurf will be the SASA.
On Wed, Sep 23, 2009 at 3:26 PM, Ganesh Kamath <gkamath9173.gmail.com>wrote:
> For a trajectory. The file is a mdcrd file format of AMBER. I could also
> convert the mdcrd file
> to a bunch of PDBs.
>
> thanks,
> ganesh
>
> On Wed, Sep 23, 2009 at 3:20 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > for a snapshot, or a full trajectory? what format are the coordinates?
> >
> > On Wed, Sep 23, 2009 at 3:07 PM, Ganesh Kamath <gkamath9173.gmail.com
> > >wrote:
> >
> > > Hi Amber Users,
> > >
> > > Could anyone tell me how to calculate the solvent accessible surface
> > areas
> > > for a protein in explicit water.
> > >
> > > thanks,
> > >
> > > ganesh
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 23 2009 - 13:00:02 PDT
