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Re: binding energy calculations -- summary (fwd)
Sender: bruce_bush@merck.com (Bruce Bush)
Subject: WSN: Re: binding energy calculations -- summary
Binding energy calculations in simplified water --
==> Summary of responses <==
On Feb 9, I posted a REQUEST to the Water Science Network:
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Subject: Binding energy calculations in water solvent
To: water@gibbs.oit.unc.edu
I would be grateful for information, anecdotes, citations, etc.
on attempts to calculate ENZYME-INHIBITOR BINDING FREE ENERGY
with *simplified* or *continuum* solvent models,.. allowing solutes.. to move.
This query is not directed especially toward full-fledged perturbation (FEP)..
I'm more interested for the present in SIMPLIFIED WATER models
that may sample wider conformational changes of solutes.
: : :
Information on GOOD TRIES, NEAR-MISSES, PUZZLING BEHAVIOR (not only SUCCESSES)
would be of interest to the whole community, I'm sure.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Here's a SUMMARY of responses to date. Further responses are welcome.
Special thanks to those who posted to the whole WSN group.
bruce_bush@merck.com (908) 594-6758
<< 1 >>
From: "Jeffry D. Madura" <madura@moe.chem.usouthal.edu> Fri 10 Feb 1995
We are in the process of writing a paper on the types of calculations
you have an interest. We have done POLARIS (A. Warshel's program) and
UHBD (A finite-difference approach) free energy binding calculations on
the enzyme-inhibitor complex of carbonic anhydrase with 7 different
sulfonamides. The results, which I don't have in front of me right now,
look very good. In the POLARIS case the inhibitor was allowed to move
via dynamics in the field of solvent. In the UHBD approach, we performed
in vacuo dynamics using QUANTA[/CHARMM].. captured several configurations and
computed the free energy of binding using UHBD through the QUANTA/UHBD
interface. We will most likely redo the UHBD calculations with the
solvent field turned on during the dynamics once I am able to modify the
UHBD program to handle prot[ei]ns. .. Mike Gilson and I have in press (JCC)
a paper on coupled FDPB/molecular mechanics and dynamics paper. ...
Address: Dept of Chemistry University of South Alabama Mobile, AL 36688
Phone: (334) 460-7430 FAX: (334) 460-7359
<< 1a >>
[ I asked questions on the calculations and Jeffry provided useful details...]
From: madura@moe.chem.usouthal.edu Fri Feb 10 11:42:50 1995
> whether UHBD displays any jumpiness [as solutes move slightly or as
> function of grid placements] , and how you eliminate it ....
Yes we see some jumpiness. What we have done is to perform a short
molecular dynamics run of 2-3 ps at 300 K. Then every .5 ps we take the
configuration and perform a FDPB free energy binding calculation... First with
a coarse grid of 1.0 A followed by a fine grid of 0.25 A. .. a 60 x 60 x 60
grid. Once all of these calculations are done we average the binding
energy results. The variation between binding results in some cases as
small as 3 kcal/mol to 9 kcal/mol. When averaged we obtain free energies
of binding within 1-2 kcal/mol of the experimental numbers.
. In my case the inhibitor is buried deep inside the active site. I
don't..have to worry much about a water .. between .. inhibitor and ..protein.
> .. gradients of solvation energy as part of the force. This is a nice goal,
> but a tricky one. Does UHBD provide correct forces? ...
Mike Gilson has actually worked out the best way to evaluate the grid
forces. This has been published in JPC 97, 3591 (1993). The use of
these forces is reviewed in upcoming article in Computer Phys. Commun.
paper. What we do is recalculate everything everytime an atom moves a
specified distance. It seems that 0.2 A is optimal in the small molecule
simulations we have done as our test cases. The small molecules being
dichlorethane and alanine dipeptide. I am looking to ramp up the program
to look at protein dynamics and enzyme-inhibitor complexes.
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