Subject: Summary: Surface and volume algorithms

From: Daquan Gao <[email-masked]>
Date: Tue, 22 Feb 2000 11:27:18 -0500

Hi everyone,

Let me summarize the responses again since there have been much more 
yestoday. Thanks to everyone and especially Robert Pearlman from Austin. 

My origianl question,
> Dear CCLers,
> 
> I would like pointers to fast algorithms(preferentially analytical) of
> computing the surface areas of molecules? Any idea is also
> appreciated.
> 

First is a quest for answers,

From: Renxiao Wang <[email-masked]>

On Fri, 18 Feb 2000, Daquan Gao wrote:

Dear Gao,

I will appreciate it if you give me a copy of all the answers you got. As
far as I know, there is few analytical algorithms for calculating surface
and volume.

Good luck!

------------------------------------------------------------------------
| Dr. Renxiao Wang                                                     | 
------------------------------------------------------------------------
| Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104  | 
| University of California Los Angeles     | Los Angeles, CA90066      | 
| Los Angeles, CA 90024                    | U.S.A                     | 
| Phone: 310-8250269 (Lab)                 | Phone: 310-3904638 (Home) | 
------------------------------------------------------------------------
| E-mail: [email-masked]                                        | 
| WWW: http://zimbu.chem.ucla.edu/~arthur/                             |
------------------------------------------------------------------------

Answer 1,
##############________________
From: "Martin,Yvonne" <[email-masked]>

Try the programs by Robert Pearlman. Savol2 I think is the most recent one.
You can get it from QCPE.

Yvonne Martin

Another request ,
##________________
From: "Dr. Sudhir A. Kulkarni" <[email-masked]>

Hello,
    Please summarize answers you get for the list or send copies to me.
Thanks.

Sudhir

Answer 2,
#################_____________
From: Thomas Huber <[email-masked]>

Daquan,

I think your question was a bit too general for the list.
Depending on your problem there are several approaches to do surf/vol
calculations.
In Protein systems the program suite of Mike Connolly is quite popular,
and it is analytical, but it costs some $500.
If you need fast analytical surfaces for visualization, try to look at the
VMD program system from Klaus Schulten's lab. There is an interface to a
program called surf. Quite fast, analytical and free.
Please specify your needs. There might be other tools (eg my molgeom6
software, but it is not yet ready for public release).

Hope this helps!

Thomas

-----------------------------------------------------------------------------
Dr. Thomas Huber                       Institut fuer Stoffwechselbiochemie
Tel.: +49(89)5996-462                  der Universitaet Muenchen
FAX:  +49(89)5996-415                  Vorstand Prof.Ch.Haass
email [email-masked]     Schillerstrasse 44
                                       D-80336 Muenchen

Answer 3,
#######################_______________
From: [email-masked]

Hello from sunny Austin, TX --

Recently, there have been a number of inquiries regarding software
for calculating molecular surface areas, molecular volumes, and atomic
contributions thereto.  The most recent posting (from Daquan Gao) was:

> This is the only response I got. Thanks to Yvonne Martin! I believe
> now that QCPE is the first place to look for this info. 
>
> Daquan Gao
>

> Try the programs by Robert Pearlman. Savol2 I think is the most recent
> one.  You can get it from QCPE.

Our community owes a lot to Yvonne Martin, both for her own contributions
and for the frequency with which she replies to such inquiries by offering
pointers to a wide variety of useful software.

In this case, however, the pointer is out-dated.  Please do *NOT* use the
old version of our surface area and volume software from QCPE.  It has not
been updated (or fixed) in many years.  Instead, please send a request to
me ([email-masked]) and I will reply with instructions for
down-loading a much newer, much nicer version called "Savol3".  

Savol3 provides extremely rapid, analytic calculation of both surface area
and volume for molecular surfaces and solvent-accessible surfaces.  In
addition to partitioning both the surface area and volume into rationally
defined atomic contributions, Savol3 also partitions the surface area and
volume into polar/non-polar contributions (based either on user-specified
charge thresholds or on the standard but crude hetero/non-hetero basis).

We currently provide Savol3 for use on SGI workstations (but could be
talked into providing it on other platforms if broad-based need exists).
We will soon offer a version which will operate on SMILES or 2D MDL SDfile
input.  Meanwhile, please note that Savol3 currently requires 3D molecular
structures as input.  These can be provided in PDB format or in Tripos' 
mol2 or mol1 format.  I/O can be specified using unix command-line options
or can be provided in response to prompts issued by the program.  
Alternatively, since we provide an object library and source code for an
example calling routine, the 3D structure and other I/O issues could be 
handled via an argument list (without concern for 3D file format).

Best wishes,

  -- Bob Pearlman

Answer 4,
########################________________
From: [email-masked]

Also try GEOPOL from QCPE.  It is used in several other programs, including
solvated geometry optimizations.

John McKelvey

From: [email-masked]

Daquan,
Now I feel guilty I'd meant to reply to your original post. The original
Connolly surface program is available from QCPE (#429) another possibility
is MSMS for solvent excluded surfaces
(www.scrips.edu/pub/olson-web/people/sanner/html/msms_home.html).
hope this helps,
-david
David Reichert, Ph.D.
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: [email-masked]
voice: (314) 362-8461
fax: (314) 362-9940