Subject: Re: MEAD

From: "Jesus M. Castagnetto" <[email-masked]>
Date: Wed, 16 Sep 1998 15:39:55 -0700 (PDT)

Hello all,

Below is the response that Dr. Bashford sent to Fernando L. Barroso
w/ respect to his questions about MEAD.

Dr. Bashford asked me to also forward this to the CCL list.

Regards.

=====
     Jesus M. Castagnetto, Ph.D. - [email-masked]
TSRI, Dept. of Molecular Biology |"Activation Energy: The useful
10550 N. Torrey Pines Rd. MBP326 | quantity of energy available
       La Jolla, CA 92037        | in one cup of coffee."
       Phone: 619-784-8582           Fax: 619-784-2289
        Lab: http://www.scripps.edu/research/metallo/
  MetalloDB: http://metallo.scripps.edu/index.html
Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/

---------- Forwarded message ----------
Date: Wed, 16 Sep 1998 14:58:59 -0700
From: Don Bashford <[email-masked]>
To: Fernando Luis Barroso da Silva <[email-masked]>
Cc: [email-masked], [email-masked]
Subject: Re: MEAD 

Dear Fernando,

Here are the answers to your questions.  A freind tells me you posted
to the Comp Chem list also, so I'll have him post my answer there too.

Don
---------

The references for MEAD are:

D. Bashford & K.  Gerwert (1992) "Electrostatic Calculations of the
  pKa Values of Ionizable Groups in Bacteriorhodopsin"
  J. Mol. Biol. vol. 224 pp.  473-486
D. Bashford.  "An Object-Oriented Programming Suite for
  Electrostatic Effects in Biological Molecules" In Yutaka Ishikawa,
  Rodney R. Oldehoeft, John V. W. Reynders, and Marydell Tholburn,
  editors, "Scientific Computing in Object-Oriented Parallel
  Environments", volume 1343 of Lecture Notes in Computer Science, pages
  233--240, Berlin, 1997. ISCOPE97, Springer.

The first one is mainly a description of pK calculations, but it is
the first paper where we announce the existence and availability of
MEAD.  The second one is an outline of the design of the MEAD
programs, and how "object-oriented" ideas were used.  If the second
one is not in your library, I can email you the LaTeX source for it.

The MEAD distribution itself has a README file that tells how to use
the programs.  Otherwise, that's it for documentation.  I'd like to
write some, including a detailed description of internals, but it's
hard to find the time.

There is not yet a MEAD mailing list, but I have been keeping the
email addresses names of people who contact me about MEAD so that a
list could be started.  Do people think there *should* be a MEAD
mailing list?

The distributed version of MEAD does not include support for the
non-linear Poisson Boltzmann equation, but I do have an "in house"
experimental implementation of NLPB, which just requires compiling and
linking a few more files to the existing base of code.  If anyone is
really interested in playing with this (which would probably require
some tinkering with the code), I'll it to them.

Donald Bashford
[email-masked]