Re: CCL-Program for pKa dete

["Don Gregory" <Don_Gregory.,at,.MSI.COM>]

         Reply to:   RE>CCL:Program for pKa determi
 I'd like to address one fine point in Beverly's response to
 Mamhood's pKa question.  Polaris calculates the *delta*pKa
 as a function of environmental change.  A small distinction,
 but quite an important one.   For example, should one wish
 to know how a mutated residue affects the pKa of a
 wild-type histidine in an active-side, knowing the
 wild-type pKa, *as a reference*, one can calculate
 the delta-pKa as a function of the environment change
 caused by the mutation.
 People have also used this capability to determine the
 change in metal-clusters as a function of explicit counter-ion,
 etc.
 Beverly is also correct in stating that Prof. Warshal's approach
 (using Langevin dipoles) is somewhere between atomistic
 and continum,inthat one may as as many explicit waters as one
 wishes, and they, as well as the solute (even protein for
 deltaG-binding calculations) are treated explicitly.  Over that, one may impose
 quite large volumes of grid points, each representing the position
 of a Langevin dipole.  Thus, one can mix explicit & Langevin
 regions as one wishes.
 A final note, these are delta-G's, NOT delta-delta's!  And the
 Langevin approach results in delta-G calculations that take
 10's of minutes at most.
 I don't really want to turn this into a sales/marketing tirade;
 I'm very much a believer that this isn't the place for that
 sort of thing, but I thought some technical clarity might
 be useful.
 Don Gregory
 Mgr. Application Science
 MSI
 --------------------------------------
 From: bbendik.,at,.telerama.lm.com
 Date: Thu, 10 Mar 1994 08:34:57 +0500 (EST)
 Subject: CCL:Program for pKa determination
 Mahmood -
 Molecular Simulations offers a program that calculates .delta.G of
 solvation, from which some pK values can be obtained.  The package is
 called Polaris (ref. by author Arieh Warshel).  It lies somewhere between
 an atomistic approach and a continuum approach.  It's worth looking into,
 as long as you apply it to molecules that are "reasonably" similar in
 structure.
 Regards,
 Bev
 Beverly Bendiksen
 Research Associate
 Calgon Corporation
 Pittsburgh, PA
 (412)7778862 voice    (412)7778714 fax
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