AMBER Archive (2009)

Subject: Re: [AMBER] solvent accessible surface area

From: Siddharth Rastogi (siddharthrastogi08_at_gmail.com)
Date: Thu Oct 08 2009 - 04:54:01 CDT

Hello Amber users,
I am interested to get SASA for hydrophobic groups and hydrophilic groups in
protein separately. How to get these values?.

On 9/23/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> 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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-- 
Siddharth Rastogi
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