Subject: summary of surface area&volume

From: Heather Carlson <[email-masked]>
Date: Sat, 16 Jul 94 18:42:38 -0400

I was asked to post a summary of the responses I received about
finding molecular surface areas and volumes.  I would like to thank
everyone who responded, especially those who offered copies of
their own programs!  We've decided to use Fred Richards programs
(thanks C. S. Raman) since they're a standard & he's across the
science courtyard!!

Heather Carlson
[email-masked]

SUMMARY:
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From: [email-masked] (Joe M Leonard)

I'm not sure whether Yale ever got Spartan, but if it has, we calculate
the area and volume using the same radii.  There are other codes
floating about in the PD or at QCPE, which you can probably recompile
with changed radii...

Joe Leonard
[email-masked]

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From: [email-masked]

        The program GRASP from Anthony Nicholls,
        [email-masked]
        should have an answer to your problem.

        Liisa Laakkonen

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From: [email-masked] (Max Vasquez)

Take a look at a program by Frank Eisenhaber; information below.  Good
luck.

Thank you very much for your interest in the paper
"Improved Strategy in Analytic Surface Calculation for Molecular Systems:
Handling of Singularities and Computational Efficiency"
published in Journal of Computational Chemistry, v. 14, N11,
(1993), pp.1272-1280 by Frank Eisenhaber
and Patrick Argos and the associated program ASC.

The program text in standard C for UNIX systems can be obtained from the
author in the following way (for academic use):
(1) ftp 192.54.41.168, the ftp-server is falcon.EMBL-Heidelberg.DE;
(2) login: ftp, during login give your E-mail address as password;
(3) change to the directory /pub/asc;
(4) move all files of this directory to your site, do not name your
    local directory asc (better ASC or something else to avoid interference
    with the executable asc !!);
(5) execute asc.call (calls make to make executable "asc") and
(6) use manual.int as introduction and manual.lib as command reference;

Since the time of the publication, a few improvements have been introduced.
As a result, the CPU-consumption was further reduced. The three time
thresholds for the analytical surface calculation in Tables I and II
can be corrected to the following values:
(1) 1PPT: 0.24, 1.74, 1.97
(2) 4PTI: 0.71, 3.66, 4.02
(3) 2PCY: 1.97, 7.38, 8.14
(4) 2RHE: 2.00, 7.72, 8.80
(5) 3FXN: 3.54, 11.43, 13.13
(6) 2UTG: 3.44, 11.29, 12.86 and
(7) 1CRN: 0.39, 2.46, 2.71.

The time consumption had been measured for an R3000 processor in a
SGI-workstation. The overall time dropped by about 40\% compared with
the data in the article, e.g. the cpu-time for 1CRN decreased from
4.27 seconds to 2.71 seconds.a

>From time to time I may change a few files at the ftp site because some
of the users or I myself find some strange behaviour. As long as the changes
are minor and, especially, do not touch the surface calculation section,
the version number will not be changed. It might be useful to update your
local version from time to time.

The program had been tested for ULTRIX on DEC-stations and for IRIX
on SGI-computers. It runs also under SunOS 4.1.3 if compiled with gcc !

Please, contact me by E-mail, if you have suggestions, problems
or questions. Sincerely,
Frank Eisenhaber
E-mail : IN%"[email-masked]"

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From: [email-masked] (Dirk Huckriede)

I posted a similar request like yours say half a year ago and got quite a
number of responses. One of the (Fortran) programs I obtained is able to
calculate surfaces and volumes in one run without altering the input etc.
I think it is best suited for your purposes. I left it at our anonymous
ftp server for you to collect:

ftp rulglj.leidenuniv.nl
anonymous
your mail-adres
cd pub/heather
binary
get volume1.tar

If you are not able to use ftp, please mail be, I can send you the file
uuencoded (the system manager won't like it though).
Bye !

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From: [email-masked] (Michael Schaefer)

I can't give you advice how to use Sybyl for your task, but I have a program
that calculates the solvent inaccessible volume of a molecule AND the
solvent accessible surface. Volume and surface are calculated for each
atom (output format: pdb, volume and surface in the 4th and 5th data
column). If you are interested, let me know.

Michael Schaefer

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From: David White <[email-masked]>

I am interested in getting into the derivation and coding of analytical
algorithms to calculate molecular surface areas and volumes.  The
data you ask for could be vital in my determining the effecacy of
such an algorithm.  Please summarize the repsonses!

Thanks
Dave

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From: [email-masked] (C.S.RAMAN)

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

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From: Volkhard Helms <[email-masked]>

I have used the program GRASP of Anthony Nicholls from Barry Honig's group
a few times (I'm no expert with it though) and it is very easy to calculate
both molecular surfaces and volumes with it and also to display them.
It uses a certain set of vdW parameters for both cases, and one can also
modify this set.
Hope this helps.

Volkhard Helms

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From: [email-masked] (Graham Hurst)

The ChemPlus set of extensions to HyperChem includes a QSAR Properties
module that can calculate surface area and volume using the same radii.
The radii are kept in a text file that you can edit if you want to use
different values.  You can also drive the calculation from a Windows
spreadsheet program (such as Excel) to collect volumes and surface areas
for a set of molecules into a spreadsheet. It can also calculate hydration
energy, Log P, refractivity, polarizability, mass and partial atomic
charges using published empirical methods.

For more information send email to [email-masked].

Cheers,
Graham

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From: [email-masked] (Chris Chen)

Hi,
You may like to try QUANTA from MSI and VOID from QCPE
for your calculation.
Chris
[email-masked]

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From: HUTCHINS%CMDA <[email-masked]>

   Another program to try is SAVOL by Robert Perlman at the University of Texas
at Austin.  I believe this is readily available from him.

       Charles Hutchins
       Abbott Laboratories

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From: "J. Eric Slone" <[email-masked]>

Please take a look at a product which I market, a demo of which is in
ccl.net, /pub/chemistry/software/MS-DOS/MOLGEN-demo.  It can handle what
you are looking for, plus a lot more.  And it will read your Sybyl
files!  Let me know if you are interested (academic pricing is $290).

Eric

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