AMBER Archive (2008)

Subject: AMBER: GB versus explicit medium

From: Francesco Pietra (
Date: Mon Nov 24 2008 - 03:39:58 CST

Hi all:
Is any experience in carrying out long MD simulations for
transmembrane proteins under both GB conditions and explicit

This question because I am carrying out MD with a large transmembrane
protein, composed of several identical units and carrying a docked
small protein (docked in accordance with physiological data) in the
extracellular part. MD under GB conditions after a careful
minimization and heating to 300K. Force field ff99SB.

MD under GB at 300K
with restraint on Cl-
using pmemd in amber10
  imin=0, irest=1, ntx=5, ntb=0,
  ig=-1, igb=5, nrespa=2, ntc=2,
  ntf=2, ntt=3, gamma_ln=2.0,
  nstlim=30000, dt=0.002,
  ntpr=100, ntwx=100,
  tempi=300.0, temp0=300.0,
  cut=999.0, rgbmax=999.0,
 Keep Cl- 427 restrained
RES 427

I understand that, forced by the huge system, I am using rather
drastic conditions (dt=0.002, nrespa=2), though I was badly surprised
to see the initial portion of one of the chains of the pore region
undergoing a 90 degrees bent at SER 14 (14 from the beginning of the
chain, while the chain continues for ca 23 amino acids in the pore
region). EPTOT EKTOT and ETOT remain constant. The extracellular
portion and docked small protein also undergo some conformational
adjustment, though, no "distortion" of the system occurs.

In another approach, for different reasons, I isolated the pore region
(with a small molecule docked in; docked in accordance with
physiological data)), cutting away the extracellular portion and
restraining the ends of the chains at the end of the pore region.
Under periodic conditions, in a hydrated POPC membrane, for a much
longer MD than the above, no distortion of the pore region occurred

Production MD, restraining
capping groups
  imin=0, irest=1, ntx=5,
  nstlim=100000, dt=0.002,
  cut=10, ntb=2, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
 Keep ACE 79 restrained
RES 79
many other capping groups restrained.

I wonder whether this may be a limitation of GB or there is evidence,
or suspicion, that setting up was not adequate. Surely, if the GB
simulation has to be made some fold slower that it is, the simulation
could hardly be carried out for an adequate time.


francesco pietra
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