From: DEEPESH AGARWAL (deepesh.iitd_at_gmail.com)
Date: Wed Jul 02 2008 - 06:13:59 CDT
Dear NAMD users,
I have done production run for 1 ns for both the enzymes i.e. wild
type and its single amino acid polymorph. The water box was created
with a layer of 5 A from extreme co-ordinates of atom in each
direction but during course of simulation some of the part of the
protein came out of the box. Also when we analyzed the output files
radius of gyration for wild type increased after 700 ps and it was
increasing for mutant from 0 ps. Can there be any problem in
simulation run due to which we had this lil weird results??
Also i want to draw topology diagram of of these proteins at these time
steps. I downloaded TOPS and software but It aborts run after a short
while due to some 'memory corruption'. Their server is presently not
available for online diagrams. Can u suggest some other tool for it.
Thanks a lot.
Deepesh
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