I am attempting to run unrestrained MD on a small glycopeptide ( 9 amino
acid and 4 GalNAc) in explicit solvent using parm94, glycam04l (the
latest version) and AMBER8, however I am having problems with backbone
stability at the first glycosylated threonine. The most obvious symptom
of the instability is that the HA-CA-CO-O dihedral angle in the first
threonine switches from ~ -130 to ~ 60 degrees after several
nanoseconds, resulting in what could best be described as a 'kink' in
the glycopeptide.
Some important notes about the system and MD parameters:
This is definitely not a switch to the cis configuration
1 fs timestep.
The glycosylated threonine in question is preceded by two prolines, and
followed by 3 more glycosylated THR's and then the rest of the peptide.
The starting structure was initially produced with xplor using NOE and
coupling data and approximates a beta-strand across the THR's.
I am using a truncated octahedron box with a 'radius' of 9 angstroms
along with TIP3 water, PME and constant pressure.
The system temperature was run up to 300K over 20 ps with weak
restraints on the glycopeptide
I have attempted to stabilize the peptide by adding bulk (in this case 4
Ala's on each end) to the glycopeptide, but without success.
Run using 4 processors of a SGI/Linux machine
here is the sander input file for the unrestrained dynamics:
&cntrl
imin=0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 10,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 1000000, dt = 0.001,
ntpr = 200, ntwx = 200, ntwr = 200
/
I would be grateful for any suggestions and/or for the pointing out of
any glaring errors.
Andrew Borgert
Biophysical Sciences and Medical Physics
University of Minnesota
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Received on Sun Jun 03 2007 - 06:07:10 PDT
