Subject: macromodel and GRASP questions

From: Michael Dooley <[email-masked]>
Date: Thu, 02 Apr 1998 11:38:35 -1000

Hello CCLer's,
	macromodel question: I'm optimising a batchmin com file at the moment
that does a monte carlo conformational search.  The structures I'm
looking at are peptides, so I would like to use a torsion selection
function to favor random torsion angles near to the trans and cis minima
of the peptide bonds.  Is there a way to set up the opcode MCTS to do
this? Or some other way?

	GRASP question: Having some problems with display of dipole moments.  I
read in a pdb file and set full crg, calculate and display the dipole
moment... no problems.  I repeat this on the second pdb file... no
problems, but when I read in the third pdb file and calculate the dipole
moment, the first protein's dipole moment shifts.  I haven't tried
reading in a fourth pdb file and calcuating the d.m. to see what
happens.  What I'm trying to do is compare the dipole moment of a group
of overlayed structures.  I'm not sure what's going on!
        In addition, I have a small peptide for which I calculated and
displayed a dipole moment.  I then mutated all of the positively charged
residues on one face of the peptide (3 in all) to glutamate residues to
create a mutant peptide, and calculated the dipole for this molecule
(rereading the full.crg file).  It superimposed PERFECTLY with the
dipole of the unmutated molecule.  Intuitively, this seemed odd.  Am I
doing something wrong?
	Can someone suggest another program that calculates and displays dipole
moments of peptides and proteins?

Cheers
Michael

-- 
Michael Dooley PhD
Centre for Drug Design and Development
The University of Queensland
Brisbane Qld 4072 Australia
[email-masked]