[gmx-users] Using R.E.D. charges with OPLS AA

Ran Friedman r.friedman at bioc.uzh.ch
Thu Mar 26 09:13:49 CET 2009


HF with 6-31G usually provide a good start for getting OPLS charges:
   Author = {Jorgensen, W. L.  and Maxwell, D. S. and Tirado-Rives, J.},
   Title = {Development and Testing of the {O}{P}{L}{S} All-Atom Force
Field on
Conformational Energetics and Properties of Organic Liquids.},
   Journal = {J Am Chem Soc},
   Volume = {118},
   Pages = {11225-11236},
 Year = {1996} }

How you assign your charges to the molecule is another issue. I normally
fit the partial charges to the electrostatic potential around the
molecule. RESP was indeed developed with AMBER, but I don't know if the
charges are so different.

Good luck,

DimitryASuplatov wrote:
> Hello,
> I need to simulate a protein with deprotonated Tyr (HH hydrogen should
> be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the
> charges. 
> 1/ The problem is that to my understanding RESP charges apply to AMBER
> only. Am I correct?
> 2/ Can I use R.E.D. charges with OPLS AA?
> 3/ If not how can I recalculate them to fit the OPLS AA?
> 4/ Any Tyr-Deprot topology already available??? 
> Thanks, I appreciate your time.
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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