Re: [AMBER] Atom Mask in QMMM calculation

From: Goetz, Andreas <>
Date: Mon, 4 Jun 2018 01:29:59 +0000

The QM/MM interface checks the first letter and the atom mass. Please check that you have a reasonable mass for Si in your prmtop file.

All the best,

Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771

On Jun 3, 2018, at 1:29 PM, emanuele <<>> wrote:

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 "" 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 - 19:00:02 PDT
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