[AMBER] Water flexibility in QM/MM simulation

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Tue, 16 Aug 2016 18:27:14 +0200

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
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