[AMBER] Atom Mask in QMMM calculation

From: emanuele <falbo.emanuele.gmail.com>
Date: Sun, 3 Jun 2018 21:29:48 +0100

Dear Administration,

I am trying to run a QMMM dynamics by interfacing AMBER to ORCA. My
molecule is solvated by the TIP3P water model, and the former is treated
by the QM part, while the water is handled by the MM. By the way, my
issue is that AMBER read the a Sulfur atom in place of the Silicon atom,
present in the solvated compound. I know that the amber mask work at
most with two letters. In fact, the Na atoms, added as counter ions by
sander,  are  included.

This is my "file.in" for the Dynamics.

   300K constant temp QMMMMD
   imin=0, ntb=1
   cut=8.0, ntc=2, ntf=2,
   tempi=300.0, temp0=300.0,
   ntt=3, gamma_ln=1.0,
   nstlim=1000, dt=0.002,
   ntpr=1, ntwx=1,ifqnt=1
  qmmask='.1-57',       #the Si atom is the number 53
  qm_theory='EXTERN',    ! Use external QM program
  qm_ewald=0, qm_pme=1

Have you got any idea of how to fix this problem.

Kind Regards,


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Received on Sun Jun 03 2018 - 14:00:03 PDT
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