LES problem

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Jul 07 2009 - 00:30:50 CDT

I'm trying to do locally enhanced sampling of O2 diffusion through a globin.
The active part of my psfgen prep file looks like this (it's headed by a bunch
of aliases because the structure was supplied with nonstandard HEME atom
names I won't reproduce here. The sections I have not supplied DO work correctly
for normal MD):
segment A {
   first NTER
   last CT2
   pdb chaina.pdb
coordpdb chaina.pdb A
segment HA {pdb hemea.pdb}
coordpdb hemea.pdb HA
segment OA {pdb o2a.pdb}
coordpdb o2a.pdb OA
# do not bind O2 for LES
#patch PLO2 OA:1 HA:900 A:82
patch PHEM A:82 HA:900
regenerate angles dihedrals
multiply 5 OA:1:O1 OA:1:O2
writepsf aida5.psf
writepdb aida5.pdb
I get 5 copies of O2 in the pdb file. They have the same cartesian coords & they're written
a little oddly, in that all copies of the first O are followed by all copies of the 2nd, instead of
grouping the residue together. I found that on solvating & ionizing, the cartesian coords of
the copies are replaced by 0's & the B-factors altered. I solved that by replacing the incorrect
values in the solvated, ionized pdb file with the original values, after checking that the cartesian
coords of the heme had remained the same.
I pre-equilibrated the system by minimizing the water with protein, heme & O2 fixed. Then I
heated from 0 to 300K with the same set of fixed atoms. Then I did a short MD (0.2ns) with only the O2 fixed,
and finally I started the MD. It's gotten to 0.6 nsec & I thought I'd have a look at the trajectory
so far, in case something's gone horribly wrong. The first 4 copies of O2 behave nicely, but in the 5th
copy, the Os separate - as in >10A apart.
What, please, am I doing wrong?
Irene Newhouse

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