Subject: summary: opls for tryptophan

From: uccatvm <[email-masked]>
Date: Tue, 6 Feb 2001 19:44:41 +0000 (GMT)

Hi CCL'ers,

Recently I asked the following question:

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I am trying to get an OPLS potential for tryptophan. Jorgensen's paper
on OPLS potential functions for proteins (W.L. Jorgensen, J. Tirado-
Rives, J.Am.Chem.Soc. 110, 1657, 1988) contains OPLS parameters
for tryptophan.  According to the paper, standard geometries were used.
However, I can't find standard values for all the tryptophan
bond lengths and angles. Could someone give me a pointer where to
find them?

Secondly, as far as I am aware, there is no all-atom OPLS potential
for tryptophan (the 1988 potential uses united atom CH groups). 
Is this correct?
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Apparently, I was wrong about the non-availability of an all-atom
OPLS potential for tryptophan. 

I would like to thank Daniel Price for pointing me to the supporting 
information belonging to Jorgensen et al.'s paper on the "Development 
and Testing of the OPLS All-Atom Force Field on Conformational Energetics 
and Properties of Organic Liquids" ,JACS 118, 11225-11236 (1996), and
Willem P van Hoorn for pointing me to the information on Jorgensen's
web site. I further want to thank Patrik Johansson for sending me
his SCF/6-31G* geometry of tryptophan. Below are the replies from
Daniel Price and Willem van Hoorn:

Daniel Price:
=============================
JACS (1996) 118:11225-11236
"Development and Testing of the OPLS All-Atom Force Field on
Conformational Energetics and Properties of Organic Liquids" Supporting
Information

Non-bonded parameters (all-atom model) for all functionalities found in
proteins are in the supporting information.  Tryptophan is in Table 4.

Also, under the heading Gas-phase structures:  "The average differences
between RHF/6-31G* and OPLS-AA results are 0.01 A for bond lengths, 2deg
for bond angles and 1deg for dihedral angles."  I would expect a 6-31G*
minimization would yield an adequate geometry for rigid calculations.
Bonded parameters are available for the entire OPLS-AA atom palette for
flexible simulation as well.

Willem van Hoorn:
=============================
There definitely is an OPLS-AA force field for all protein residues. If you
go to the Jorgensen group homepage (zarbi.chem.yale.edu) you can download
the MCPRO manual and see for yourself. The exact geometries/parameters are
not in there though... (you can find them in the MCPRO distribution).

Best wishes,

Tanja
-- 
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     Tanja van Mourik                                                
     Royal Society University Research Fellow
     Chemistry Department 
     University College London    phone:    +44 (0)20-7679-4663      
     20 Gordon Street             e-mail:   work: [email-masked] 
     London WC1H 0AJ, UK                    home: [email-masked]     

     http://www.chem.ucl.ac.uk/people/vanmourik/index.html
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