Hi all. I am doing a TI caltulation in order to obtain the free energy
values associated with the loss of a proton from a hydroxyl group bound to
a zinc atom coordinated with 3 other aminoacids. System 1 comprises of a
water molecule bound to the zinc atom, and system 2 is the hydroxyl group.
When I run qmmm simulations, using DFTB, of both systems separately, the
system stays intact, i.e. no bonds are broken and both the water and the
hydroxyl stay bound to the zinc atom ( as was expected). But as soon as I
star with the TI simulation, the hydroxyl group always drifts away.
Sometimes the oxygen atom stays and the hydrogen goes for a walk. This
happens only on TI simulations and the water system stays intact. I have
tried different sizes of qm region, different cutoffs, tried several
different starting structures ( minimized, equilibrated, thermalized etc)
and the result is almost always the same. Below is the input file for the
hydroxyl group system. I thought about restraining the hydroxyl group using
the nmropt module. Can I use the dvdl_norest flag to ignore those
restraints in the energy calculation? Please let me know if you need any
other detail from the simulation and/or if you need/want any file from the
inputs.
Thank you
Fabrício Bracht
TI of hydroxyl group step 1
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 8.0,
ntr = 0,
ntc = 2,
ntf = 1,
temp0 = 298.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 1000000, dt = 0.0005, ntave = 100,
ntpr = 100, ntwx = 100, ntwr = 100,
ig = 10703, ioutfm = 1, iwrap = 1,
icfe = 1, ifsc = 1, clambda = 0.01592,
ifqnt = 1, scmask = ':342', idecomp = 0, nmropt = 0,
/
&qmmm
qmmask=
':200,255,258&!.CA,C,HA,O,N,HN,H|:341,342|(:202,204&!.CA,C,HA,O,N,H)'
dftb_3rd_order = 'PA'
qmcharge=-1,
qm_theory='DFTB',
qmshake=0,
qm_ewald=1, qm_pme=1
qmcut=9.0
writepdb=1
/
Receptor residues
RRES 1 7853
END
Printing
RES 1 342
END
END
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Received on Sat Feb 02 2013 - 12:00:03 PST
