Hi all:
Is any experience in carrying out long MD simulations for
transmembrane proteins under both GB conditions and explicit
environment?
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
&cntrl
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,
ntr=1,
/
Keep Cl- 427 restrained
32.0
RES 427
END
END
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
&cntrl
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,
temp0=300.0,
ntr=1,
/
Keep ACE 79 restrained
32.0
RES 79
END
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.
Thanks
francesco pietra
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Received on Fri Dec 05 2008 - 16:32:15 PST
