Subject: Rolling H charges into their heavy atoms?

From: [email-masked]
Date: Mon, 26 Apr 1999 21:20:05 -0700

Hello people,

I wanted some opinions from those well versed in the field about a practice
I've seen mentioned in some docking studies with proteins (an area in which
I'm interested).  Most PDB files have no H's mapped.  Since the ESP is
important in those studies, having some good estimate for the partial
nuclear charges is naturally important.  It appears that one can either add
the H's onto the existing structure or take a well-calculated amino acid
structure (using an ab initio program) and additively "roll" the nonpolar H
charges into their respective heavy nuclei.  In this case, those which might
H-bond seem to be treated separately (added to the structure), which makes
sense to me.  

First, is this a reasonable 1st-level understanding of the approaches to
this?  Or have I misunderstood things?

The second approach (rolling charges into the heavy atoms) would certainly
appear to be the easiest to adopt.  Is there good reason Not to do either
approach?  In both I can see an issue of accuracy for a number of obvious
reasons from the QM perspective, but wonder about the validity of this
concern on the broad scale over which these protein interactions occur.  

Any references would also be appreciated.  My apologies if this seems
trivial or mundane ... I'm quite new to all of this, and am learning it near
the back of a dark cave ...  :)  Thanks very much!

Kenward Vaughan
Professor of Chemistry
Bakersfield College
Bakersfield, CA
661-395-4243
[email-masked]  (work)
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