AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8

From: Andrew Borgert <>
Date: Wed, 30 May 2007 12:35:51 -0500

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:

  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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jun 03 2007 - 06:07:10 PDT
Custom Search