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WSN: PC-based aqueous modeling (reposted from CCL)
Date: Thu, 21 Apr 94 13:37:53 PDT
From: billg@scg.fai.com (Marketing)
Subject: summary-aq.modeling
Netters,
I want to thank everyone who replied to my request for information about
PC-based codes for aqueous modeling. The responses are summarized below.
-Bill Glauser
=============================== Original question =============================
Netters,
I am looking for a Windows-based PC software package that computes
various properties of aqueous systems. Examples include properties
such as free energies of solvation, pKa, partition coefficients,
solubilities, diffusion coefficients, etc.
My guess is that any such package would be rule-based, but perhaps
there are some that include input from quantum-chemical calculations
as well.
I believe that MSI markets a code known as "Polaris" that fulfills
a similar function on UNIX-based platforms.
I would certainly appreciate any suggestions or comments that you
may have.
-Bill
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* William A. Glauser, Ph.D. | Internet: billg@scg.fai.com *
* Computational Chemist | Voice: (610) 436-8125 *
* SuperComputer Group | FAX: (610) 430-1526 *
* Fujitsu America, Inc. | *
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Eric Sloane writes:
It's not Windows based, but I sell a product called Molgen that does
much of what you are asking for, for much less than comprable products.
It imports/exports alot of file formats, so I can take a structure from
a 2D program like ChemWindow, import it, find the lowest energy
conformer, then export it as a PDB or similar file. I then use RasWin
to view the molecule and cut/paste it into my apps.
If you're interested, I can FTP you a copy of the run-time version to
try out.
Eric
________________________________________________________________________________
J. Eric Slone Scientific Consulting Services
Serving Government & Industry Since 1982
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Chris Waller writes:
I have a couple of suggestions:
> I am looking for a Windows-based PC software package that computes
> various properties of aqueous systems. Examples include properties
> such as free energies of solvation, pKa, partition coefficients,
> solubilities, diffusion coefficients, etc.
>
To my knowledge there aren't many PC-based packages that do these
calculations (yet!), but I do recall a package named PrologP which
calculates logP's based on the additivity principle, like the clogP
program of Leo et al.
> My guess is that any such package would be rule-based, but perhaps
> there are some that include input from quantum-chemical calculations
> as well.
>
> I believe that MSI markets a code known as "Polaris" that fulfills
> a similar function on UNIX-based platforms.
>
I have used Polaris and find it somewhat limited. For example, if
one wishes to use semi-empirically derived partial charges in the
calculation, the program is only parameterized for MNDO charges.
Biosym markets a package called Delphi which I have used
over the past few years. I encourage you to look at this program
for your Unix applications.
It is possible to calculate free energies of solvation semi-empirically.
The first package to allow this was Amsol by Chris Cramer. Other semi-
empirical programs (MOPAC) have recently incorporated this functionality.
> I would certainly appreciate any suggestions or comments that you
> may have.
>
Hope this helps!
Chris
********************************************************************
*Chris L. Waller, Ph.D. PHONE 919-541-7976*
*Research Chemist FAX 919-541-5394*
*waller@thor.herl.epa.gov *
*Pharmacokinetics Branch (MD-74) *
*ETD/HERL/USEPA *
*Research Triangle Park, NC 27711 *
********************************************************************
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Andy Holder writes:
Dear Dr. Glauser,
We market AMPAC 5.0PC which runs under Windows and contains the AMSOL
models developed by Cramer and Truhlar. These models do most of what
you mentioned from a semiempirical quantum mechanical perspective. If
you would like further information, please let me know and I'll send
some propaganda along.
Andy Holder
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
DR. ANDREW HOLDER
President, Semichem
Semichem, Inc. || Internet Addr: aholder@vax1.umkc.edu
7128 Summit || Phone Number: (913) 268-3271
Shawnee, KS, 66216 || FAX Number: (913) 268-3445
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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Vitaly Khutorsky writes:
Dear Dr. Glauser,
I use for these calculations Insight and Discover programs of BIOSIM
corporation on the SiliconGraphics Iris workstation.
Vitaly Khutorsky
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Dennis Gerson writes:
Bill, also try OLI Systems in NJ. They market pc-based software for
doing biological waste process analysis in chemical engineering. Their
code calculates lots of properties.
Regards, Dennis Gerson
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