Subject: A rather strange situation

From: "Dr. Richard L. Wood" <[email-masked]>
Date: Fri, 03 Aug 2001 11:47:44 -0400

Hi all

Even though I my Ph. D. thesis work was doing molecular dynamics
simulations, I don't
claim to be an expert in the field.  That being said, I have still never
seen the following
situation which I will describe to you.  Any input or suggestions will
be most welcome and
appreciated.

I have been doing MD simulations using CHARMM on a small peptide having
27 amino acid
residues, both in vacuum and in solution.  I have also done some
simulations where the peptide
is heavily glycosylated, again both in solution and in vacuum.
Originally, the sugars were
alpha-linked, but now I have linked them beta.  The redone vacuum
calculation is ok, but the
solvated system is giving me problems.  By that I mean, when I run the
dynamics, I get nans (not a
known quantity, basically) where I would normally get a value.  Yet,
what I find is strange is that
the calculation runs, and if you look at the trajectory (i.e., run a
"movie") everything seems to look
ok.

I've tried everything I can think of, including trying to minimize the
heck out of the system.
Everything else is the same except the sugars are beta.  My theory (I
know, bad word...lol) is that it
has something to do with the conformation of the peptide and the fact
that it has all these sugars.
Initially, I had half of the peptide in an alpha-helical like
conformation (because this was a project
that someone else had started to work on, and I picked up where they
left off), and I think that the
the part that was helical (which has 4 threonine residues, btw, which
have 9 sugars attached)
allowed the sugars to interact LESS than they are now.  This increased
sugar-sugar interaction (?) is somehow driving the energy of the system
in water through the roof so to speak.  At least,
that is my theory.

Does anyone have any experience with situations like this and have a way
to work around it?  Any additional suggestions are also welcome.

Thanks,
Richard

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
Post-doctoral Associate
Department of Food Science
120 Stocking Hall
Cornell University, Ithaca, NY 14853