Dear Amber community,
It will be interesting to see a non-guided drug molecule could find its
protein target binding site(s) and/or allosteric sites if we can run
several micro-second long simulations using pmemd.CUDA.mpi , similar to
this study.
http://pubs.acs.org/doi/abs/10.1021/ja202726y
Unfortunately there are not too many method details reported in the
manuscript to follow up. We are taking some other long simulation examples
in the Amber community and other D.E. Shaw plus P.E. Vande's
publications. The proposed settings are below. Wonder if the community
could kindly offer some comments?
a. Force field: ff12SB. It seems to provide good protein stability in
Professor Case's studies.
http://archive.ambermd.org/201211/0363.html
b. pmemd.CUDA.mpi precision model: SPFP
c. solvent: TIP3 water in an 10A octahedron truncated water box
d. Minimization:
&cntrl
imin = 1,
ntx = 1,
maxcyc = 2000,
ntmin = 2,
ntpr = 100,
ntf = 1,
ntc = 1,
ntb = 1,
cut = 8.0,
&end
e. Equi 1
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 8.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 310.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.002,
ntpr = 1000,
ntwx = 25000,
ntwr = 25000,
restraint_wt = 10.0,
restraintmask = '${protein-ligand-mask}',
iwrap = 1,
ioutfm =1,
ig = -1,
&end
f. NPT equilibration ntt =3
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
ntp = 1,
pres0 = 1.0,
taup = 2.0,
cut = 8,
ntr = 0,
ntc = 2,
ntf = 2,
temp0 = 310.0,
tempi = 310.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.002,
ntpr = 1000,
ntwx = 25000,
ntwr = 25000,
iwrap = 1,
ioutfm =1,
ig = -1,
&end
g. NPT production run: the same as "equi 2" but change to ntt=1, taup =10
to avoid the NANs issue.
Many thanks,
Henry
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Received on Sun Feb 23 2014 - 23:00:03 PST
