Subject: molecular surface area and volume

From: Heather Carlson <[email-masked]>
Date: Fri, 15 Jul 94 12:10:52 -0400

Hello net -
        I am looking for a program which calculates molecular surface
area and volumes (using the same radii).  I have used Midas' "ms" to
determine surface area and Sybyl's "volume" to find volume.  The problem
is that the parameters are not the same in the two programs.  In fact,
there are 2 sets of vdw radii in Sybyl, and I'm not sure which is being
used by the volume routine.
        Is there a program which does both, or a way to have Midas
give me volumes and/or Sybyl give me surface area?  There is a "connolly"
routine in Sybyl for solvent accessable surface area, but this results in
a third set of Sybyl vdw radii.
        I just want surface area & volume calculated the same way with
the same parameters.  Is there a way to do this?

                                        Thanks - Heather
                                        [email-masked]

---

From: [email-masked] (C.S.RAMAN)
Date: Fri, 15 Jul 1994 13:44:41 -0500 (CDT)

> the same parameters.  Is there a way to do this?

What you need are the programs ACCESS (for calculating solvent
accessible surface areas) and VOLUME from Fred Richards at Yale.  I
suggest that you contact Art Perlo ([email-masked]) to obtain
an academic license (free for academia!).  Since you are in New Haven
there should be no problem.  ACCESS will let you define any probe radius
and is pretty straight-forward to use.

Yet another package called MSP (Molecular Surface Package) is available
from Mike Connolly ([email-masked]) for detailed dissection of
surfaces.

Finally, GRASP (from Tony Nichols, Columbia U.) also has various
features to manipulate surfaces.

Hope this helps
Cheers
-raman
-- 
C.S.Raman                           
UNIX Programming & Administration   
SPARC & SGI Systems                 [email-masked] - INTERNET
Department of Biochemistry          [email-masked] - CHPC
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