Subject: Summary: Molecular area of adsorbates

From: "Gurp, Ron van" <[email-masked]>
Date: Mon, 7 Sep 1998 08:36:58 +0200

Dear Netters,

Thanks for all responses to our question. Here is our summary as
promised

Ron van Gurp and Marco Linders

Our question was:

	>Dear Netters,

	>We are looking for a program that calculates the area of a
molecule,
	>which is projected on a surface. The practical background is
the
	>following: consider molecules that are adsorbed on a surface.
What is
	>the average area they occupy on that surface ? This depends of
course >on how a particular molecule adsorbs on a surface, i.e. its
orientation
	>relative to the surface. As a first estimate one may take the
average of
	>a certain number of projections (or cross sectional areas).
Does anyone
	>know of a program that calculates such projected surfaces from
a MOL,
	>XYZ, PDB or QUANTA MSF file input, or, even better, a program
which >also takes into account the preferred orientations of a molecule
on a >surface?

Jack A. Smith wrote:

Look at Craig Taverner's steric program
(ftp://hobbes.gh.wits.ac.za/pub/steric/) based on solid angles.  The
solid angle corresponds to a projection onto an enclosing sphere, but if
you set the origin far enough away from the molecule (effectively
increasing the radius of the enclosing sphere), the solid angle
projection will approach an orthogonal projection. The projected area
would be R*R*(Solid Angle), where R is the radius of the sphere (the
distance between the origin and the furthest atom).  The program will
read PDB format, and it will generate a GnuPlot plot of the angular
profile.  The program should be easily modified to give the othogonal
projection directly without resetting the origin

Donald B. Boyd wrote:

Hello Ronald,
Check out the software products of Oxford Molecular.  I think they have
a
program (for sale) that projects molecules onto a surface.  Oxford
Molecular,
QCPE, etc. have programs that calculate molecular surface areas.  See
the
appendix of Vol. 7 of Reviews in Computational Chemistry for more
details.

Dayong He wrote

Hi, Gurp: go to the page : http://www.polymer.uakron.edu/~hoon

I know he has done this. Good luck. Yong

Cory Bystrom wrote:

Two software packages you might be most interested in:

Surfnet:

http://bsmcha1.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html

MSRoll

http://www.biohedron.com/msp.html

Hope this helps,

Fuad Abdallah wrote:

Dear Ronald,

you could try surfnet 
http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
that comes free for academic users (as far as i remember) or,

icm, 
http://www.molsoft.com

a (very good) commercial solution for your problem.

Once again, many thanks. We feel our problem has been solved!!

Ron and Marco