[AMBER] QM/MM link atoms

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Tue, 31 Jul 2018 12:09:10 +0100

Dear admins,

I am running a QM/MM simulation interfacing AMBER to ORCA. My system is
composed by a molecule, treated at QM level and surrounded by Li+ atoms,
which I wish to treat at MM level.
The problem is that SANDER keeps saying me that

adjust_q=2 requires natom-(nquant+nlink)>=1 .

1. I did not specify to include link atoms, cause I don't know how to do

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
 qm_theory='EXTERN', ! Use external QM program
 qm_ewald=0, qm_pme=1

2. This is must be because the charge in file.prmtop is 24- but I used
"qmcharge=0" ( because I want ORCA to run a a calculation on a neutral

3. In fact, in creating the file.prmtop for my molecule I used the Mulliken
charges from an ORCA calculation, and the total molecule charge is 3- .
But, I want to surround it by 27 Li+ , and for this reason the total charge
will obviously be 24-.
The thing is that I can't get the Mulliken charge from ORCA for my
molecule, because the molecule 27- doesn't converge, reason why I am trying
a QM/MM run to distribute the Li around.

Do you have any idea about how this problem can be fixed ?

Best Regards,
AMBER mailing list
Received on Tue Jul 31 2018 - 04:30:02 PDT
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