Subject: Re: CCL:Surface and volume calculations

From: [email-masked]
Date: Mon, 21 Feb 2000 18:20:02 -0600 (CST)

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
>
> ---------- Forwarded message ----------
> Date: Sun, 20 Feb 2000 11:32:03 -0600
> From: "Martin,Yvonne" <[email-masked]>
> To: [email-masked]
> Subject: Re: CCL:Surface and volume calculations
>
> 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