On Thu, Oct 20, 2005, Yong Xu wrote:
>
>
> (2) what is the main difference between Molsurf using in MMPBSA/AMBER and
> MSMS program should we use SASA surface in solvation free energy
> calculation?
>
> there are always different output for those two program using the same
> probe-radius. for molecule no100.pdb, MMPBSA give out 78.269 with 1.4 A
> probe-radius
>
> BUT MSMS give out following infomation, which surface should be taken ?
> ========
> command : msms -if no100.xyzr -probe_radius
>
> ANALYTICAL SURFACE AREA :
> Comp. probe_radius, reent, toric, contact SES SAS
> 0 1.500 1.976 24.483 57.351 83.810 213.956
Note that you have a 1.4 Ang. probe for molsurf and a 1.5 Ang. probe for MSMS.
The "molecular surface area" is called SES (solvent-excluded surface) in MSMS.
If you actually use the same probe radii, you should get comparable results
from the two programs.
You can get the solvent-accessible surface (SAS) area from molsurf by the
following: add the probe radius to each of the atomic radii, then compute the
resulting molecular surface area with a probe radius of zero.
....good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Oct 20 2005 - 17:53:01 PDT
