macromodel and GRASP questions
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?
Michael Dooley PhD
Centre for Drug Design and Development
The University of Queensland
Brisbane Qld 4072 Australia
m.dooley # - at - # mailbox.uq.edu.au