Dear Amber users,
I’m running a QM/MM simulation of a protein with its ligand in explicit solvent. In the active site, a proton transfer is expected to occur between the ligand and the closest water molecules surrounding it.
In order to unconstraint the H bonds from the water molecules I’ve visually chosen as the ones “being able to react”, I’ve followed the instructions according to the following thread: http://archive.ambermd.org/201509/0414.html <http://archive.ambermd.org/201509/0414.html> (plus noshakemask and qmshake=0 in the input file as ntc=2=ntf).
Yet I wonder: are the H bonds from my water molecules effectively unconstrained?
This is my input file:
Constant Temp 300K MD QM/MM
&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=50000, dt=0.001,
ntpr=250, ntwx=200, ntwr=500, ioutfm=1,
ntc=2, ntf=2,
noshakemask = '.921-937,2650-2693,2832-2855’,
ntr=1,
restraintmask = ':170,185,@CA,C,N',
restraint_wt=5.0,
ifqnt=1,
/
&qmmm
qmmask=':188,189,199,296-299',
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qmcut=8.0,
/
I wonder this because during QM/MM minimisation with the following input, a proton transfer occurred from a water molecule to the ligand, but it hasn’t happened again during dynamics (which I’ve been running for quite some time now).
Min of the whole structure QMMM
&cntrl
imin=1,
maxcyc=10000, ncyc=8500,
cut=12.0,
ntb=1,
ntr=1,
restraintmask = ':170,185,@CA,C,N',
restraint_wt = 5.0,
ifqnt=1
/
&qmmm
qmmask=‘:188,189,199,296-299',
qmcharge=-2,
qm_theory='PM3',
qmshake=0,
qmcut=12.0,
/
I’ve also recently found that if one is going to use ‘flexible” water models, then when preparing the topology files FlexibleWater should be set “on", which I didn’t do because I didn’t know about it then. So I wonder: are the HW-OW-HW angles missing from my topology file?
Thanks in advance for any insight,
Ruth
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Received on Tue Aug 16 2016 - 09:30:03 PDT
