AMBER Archive (2009)

Subject: [AMBER] Can bond clevage & formation conducted by qm/mm via sander?

From: sychen (u8613020_at_msg.ndhu.edu.tw)
Date: Tue May 05 2009 - 08:12:32 CDT

Dear all,

I'm a beginner for using qm/mm md in AMBER, and I tried to use qm/mm
function by sander to watch bonds clevage & formation.

Input for running is as below,
#####################
50ps qm/mm input for GLU, ASP & part of ligand
 &cntrl
   imin=0, dt=0.0005, ntr=0, ntb=2, nstlim=100000,
   irest=1, ntx=7,
   ntc=1, tol=0.0000001, ntf=1,
   ntp=1, taup=2.0,
   ntt=1, tautp=2.0, vlimit=10.0,
   cut=10.0,
   jfastw=4,
   ntpr=10, ntwr=10, ntwx=10,
   nscm=2500, iwrap=1,
   ifqnt=1,
 /
 &qmmm
  qmmask='@1757-1763, 2002-2007, 5498-5539, 5667-5669',
  qmcharge=-1,
  qm_theory='PM3',
  qmshake=0,
  qmcut=10.0,
 /
#####################

However, there's no change for proton transfer (ie, GLH --> GLU & proton
transfer to ligand) by monitoring the corresponding distance variation,
and it remained stable.

I'm wondering if such thought is reasonable? Could anyone provide me
with some suggestion or reference?

Thank you in advance!

Sincerely,
yuann

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