Dear Amber users,
I am having problems minimizing and equilibrating a metalloprotein with Zn coordinated to 2 histidines, a glutamate and a TIP3p water molecule using the bonded model. During the solvent minimization everything is fine because solute is fixed. When releasing the restraints the Zn-bound water moves slightly so that its hydrogen overlaps with the Zn-bound glutamate's OE1. Bill Ross previously suggested that I apply SHAKE to keep TIP3 H's within the boundary of the O vdw
radius, since the H's have no radius. However, when applying SHAKE with no atom restraints the minimization is stuck on a solvent TIP3p oxygen with no energy change over the steps and eventually terminates with a LINMIN error.
I managed to proceed with minimization by keeping the 3 atoms of the Zn-bound water restrained with a weight of 50.0 and SHAKE off. This was followed by heating and equilibration of the solvent at 300K and everything looked fine. Unfortunately once I release the restraints the equilibration terminates with a SHAKE error. Atoms 12494 and 12496 are the O and H2 of the Zn-bound water and I'm guessing this error is triggered because they were restrained during all minimization steps. Is this a likely cause?
vlimit exceeded for step 32; vmax = 42.6847
vlimit exceeded for step 33; vmax = 60.6431
vlimit exceeded for step 38; vmax = 26.7420
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 4 6057 12494 12496
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Could I prevent the overlap of the water and glutamate atoms during minimization (without SHAKE) by applying a distance restraint to keep them apart while minimizing the water atoms along with the rest of the system?
If so, how could I include this in my min.in? I've looked at the manual and saw mention of nmropt but unsure of how to write the restraint.
Here are my input files:
minimization 1 of solvent:
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 5000, ncyc = 2500, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntp = 0,
ntwx = 50,
ntpr = 50,
ntwr = 5000,
ioutfm = 1,
iwrap = 1,
ntr = 1, restraintmask='!:WAT,Na+', restraint_wt=50.0
/
minimization 2 of system (WAR = Zn-bound water):
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 20000, ncyc = 10000, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntp = 0,
ntwx = 100,
ntpr = 100,
ntwr = 20000,
ioutfm = 1,
iwrap = 1,
ntr = 1, restraintmask=':WAR', restraint_wt=50.0
/
heating solvent:
# Control section
&cntrl
imin = 0,
irest = 0,
ntx = 1,
nstlim = 300000, dt = 0.002,
ntc = 2, ntf = 2,
tempi = 10.0, temp0 = 300.0,
ntwx = 5000, ntpr = 5000, ntwe = 5000,
ntb = 1, ntp = 0,
ntt = 3, gamma_ln = 2, ig=-1,
cut = 10.0,
ntxo = 2,
ioutfm = 1,
iwrap = 1,
nmropt = 1,
ntr = 1, restraintmask='!:WAT,Na+', restraint_wt=50.0
/
&wt type='TEMP0', istep1=0, istep2=100000, value1=10.0, value2=100.0/
&wt type='TEMP0', istep1=100001, istep2=200000, value1=100.0, value2=200.0/
&wt type='TEMP0', istep1=200001, istep2=300000, value1=200.0, value2=300.0/
&wt type='END'/
equilibration 1 of solvent:
# Control section
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2, ntp = 1, pres0 = 1.0, taup = 2.0,
cut = 10.0,
ntc = 2, ntf = 2,
temp0 = 300.0,
ntt = 3, gamma_ln = 2, ig = -1,
nstlim = 100000, dt = 0.002,
ntwx = 1000, ntpr = 1000, ntwe = 1000,
ntwr = 100000,
ioutfm=1,
iwrap=1,
ntr = 1, restraintmask='!:WAT,Na+', restraint_wt=10.0,
/
equilibration 2 of system:
# Control section
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2, ntp = 1, pres0 = 1.0, taup = 2.0,
cut = 10.0,
ntc = 2, ntf = 2,
temp0 = 300.0,
ntt = 3, gamma_ln = 2, ig = -1,
nstlim = 100000, dt = 0.002,
ntwx = 1000, ntpr = 1000, ntwe = 1000,
ntwr = 100000,
ioutfm=1,
iwrap=1,
ntr = 0,
/
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Wed Sep 20 2017 - 07:30:03 PDT
