Thank you very much Andreas. Even though my file.mol2 contains the Si atom,
after tleap I got an atomic number of 16 ( sulfur atom) in the file.prmtop.
However,
I changed manually the atomic number of the Sulfur (16) to Silicon (14) in
prmtop file, and now it seems that ORCA reads the Si correctly.
Cheers,
Emanuele
2018-06-04 2:29 GMT+01:00 Goetz, Andreas <agoetz.sdsc.edu>:
> 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,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
> Web: www.awgoetz.de<http://www.awgoetz.de>
>
> On Jun 3, 2018, at 1:29 PM, emanuele <falbo.emanuele.gmail.com<mailto:
> falbo.emanuele.gmail.com>> 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 "file.in" for the Dynamics.
>
> 300K constant temp QMMMMD
> &cntrl
> 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
> /
> &qmmm
> qmmask='.1-57', #the Si atom is the number 53
> qmcharge=0,
> spin=2,
> qm_theory='EXTERN', ! Use external QM program
> qmshake=1,
> qm_ewald=0, qm_pme=1
> /
> &orc
> use_template=1
> /
>
>
> Have you got any idea of how to fix this problem.
>
>
> Kind Regards,
>
> Emanuele
>
>
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Received on Mon Jun 04 2018 - 03:00:01 PDT
