Hi Andrew,
According to the torsion curve you state, I don't think it is a
problem with Glycam since it does not include a HA-CA-C-O torsion
term. (You are using Glycam's residue OLT for your threonine?) Maybe
try different protein force fields and see if the kink still happens.
This may help you isolate the problem to particular parameters.
Another thought is maybe the proline residues before the threonine
are inducing a beta turn into the peptide, and you can check this by
plotting the phi/psi values. Or maybe the simulation is telling you
something...
Cheers,
Karl
____________________________________
Karl N. Kirschner, Ph.D.
Center for Molecular Design, Co-Director
Department of Chemistry
Hamilton College, Clinton NY 13323
____________________________________
On May 30, 2007, at 1:35 PM, Andrew Borgert wrote:
> 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 - 06:07:14 PDT
