Sir,
As suggested, I saw section 11.17. Following was written :
matrix superimpose( molecule mol, string aex1, molecule r_mol, string aex2
);
int rmsd( molecule mol, string aex1, molecule r_mol, string aex2, float r );
float angle( molecule mol, string aex1, string aex2, string aex3 );
float anglep( point pt1, point pt2, point pt3 );
float torsion( molecule mol, string aex1, string aex2, string aex3, string
aex4 );
float torsionp( point pt1, point pt2, point pt3, point pt4 );
float dist( molecule mol, string aex1, string aex2 );
float distp( point pt1, point pt2 );
int countmolatoms( molecule mol, string aex );
int sugarpuckeranal( molecule mol, int strandnum, int startres, int endres
);
int helixanal( molecule mol );
int plane( molecule mol, string aex, float A, float B, float C );
float molsurf( molecule mol, string aex, float probe_rad );
But how shall I exactly use this? Also whether the whole thing is required
or only the last line is important for calculation of sasa ?
Can you provide me with a sample script which has been used for sasa
calculation? What will be the commands to run the script? I'll be
calculating sasa for the first time, so was seeking your kind and lucid
explanation in order it understand it better.
Thanks a lot in advance...
Asfa.
On Thu, Jul 29, 2010 at 7:13 AM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jul 28, 2010, Asfa Ali wrote:
> >
> > Is there any way to calculate Solvent Accessible Surface Area (SASA) in
> > Amber? I am using Amber 9 package with AmberTools 1.3.
>
> See the "molsurf" routine, described in section 11.17 of the AmberTools
> Users'
> Manual.
>
> ....dac
>
>
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Received on Thu Jul 29 2010 - 00:00:03 PDT
