Subject: Summary: Assign Atomic Types for Small Molecules.

From: Yongxing Liu <[email-masked]>
Date: Wed, 15 Oct 1997 11:41:39 -0400

Dear CCLers, 

Thanks again for all who answered my questions. This a summary.

**** The Original Question****

I am looking for rules based on SMILES to assign molecular mechanic atomic
types( e.g. for OPLS all atom model) to a variety kinds of small organic
molecules and molecular ions(total about 300 molecules).  By doing that I
can assign atomic charges and VDW radii for each molecule atom. Would any
one please give me any information about where can I find these rules and
programs(free source code) to do this ? Or are there any alternative ways
to assign MM atomic charges and VDW radii for small organic molecules
automatically? 

**** Comments to the question ****

My goal is to assign OPLS-AA/AMBER charges and VDW radius to each atom for
my 300 molecules training set. I tried HyperChem and Insight-Buider.
HyperChem can assign AMBER types to all my moelcules, but AMBER do not have
charge parameters for all my small molecules(Unless you do the ab initio
calculation which I can not afford for all my 300 molecules). I also do not
want to write OPLS rules for InsightII Builder.  

*** Answers from Professor DOUGH ****

BABEL does conversion of simple SMILES to MM2/MM3 file formats - you should
search for it to find the places it can be obtained.

*** Answers From Professor  TJ O'Donnell ***

We published a paper on a method to assign atom types using
SMARTS, an extension of SMILES to define molecular substrucutres,
which of course include atoms.
I believe this is what you were looking for.
We have sets of SMARTS for a variety of atom-type sets,
e.g. AMBER, GRIN/GRID, etc., but not for OPLS.
The actual implementation uses an old (no longer supported)
Daylight program GCL and we have not modified the program
to work with newer Daylight versions.  However, the SMARTS
strings defining the atomic environments are entirely
compatible with recent versions of Daylight SMARTS.

A General Approach for Atom-Type Assignment and the Interconversion of
Molecular Structure
Files, TJ O'Donnell, et. al., J. Comput. Chem., 12, 209-213 (1991). 

*** Answers From Professor Richard Gillilan ***

Although FFAssign is not yet available for general use, I am interested
in any intrepid early users who would be willing put the code to a good
test (not too many please). Currently the code should reproduce all 
the charge assignments in Halgren's papers and supplementary 
material except two or three cases documented in the README (soon to 
be fixed). Many of the exotic chemical types have not been tested yet.

 The assignments are being tested against available published results
 and should agree with all values in Halgren's papers (please notify 
 me if you find exceptions). I have not yet compaired absolute energy
 values against those in commercial implementations (soon, maybe). 

Interested persons should
contact me (Richard Gillilan) [email-masked]
---------------
               >>>> FFAssign Version 0.0 <<<<

          Copyright (C) 1997 Cornell Theory Center

 FFAssign is an independent implementation of the MMFF94 force field
 written at the Cornell Theory Center. The Theory Center's Parallel 
 Processing Resource for Biomedical Scientists is supported by the National 
 Center for Research Resources of the NIH under grant # P41 RR04293. 

What does FFAssign do?

 FFAssign reads in a molecular coordinate file (in either of
 two formats) and assigns empirical forcefield parameters
 based on the chemical types encountered and supplies efficient
 basic simulation functionality suitable for inclusion in 
 user-written (C++) applications. Output files generated are
 also compatible with Trevor Hart's RESEARCH docking program.
 FFAssign is a FULL implementation of the Merck Molecular Force 
 Field (MMFF94) based on the published work of T.A. Halgren:

 T.A. Halgren. "Merck Molecular Force Field. I. Basis, Form, Scope,
 Parameterization, and Performance of MMFF94
 Journal of Computational Chemistry", Vol 17 Nos 5,6  pp 490-519 (1996)

(See also parts II-V in the same Journal and supplementary material)

*** Conclusion ***

The above answers are very helpful to me. Based on the answers, I will write
a program suitable for my purpose.

Yongxing Liu
Department of Chemistry
Wesleyan University
Middletown CT 06459

E-mail [email-masked]
Telephone: 860-685-2777(Office)
           860-343-7330(Home)
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