AMBER Archive (2009)

Subject: Re: [AMBER] solvent accessible surface area

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 23 2009 - 14:29:57 CDT

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_at_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_at_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_at_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
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