Thanks a lot for all the suggestions.
Jacopo
2016-08-31 23:15 GMT+02:00 Dr. Andreas W. Goetz <agoetz.sdsc.edu>:
> The QM/MM Hamiltonian also contains a vdW term. You should also change the
> vdW parameters, unless the atom is sufficiently far from the MM region.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Aug 31, 2016, at 9:00 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> > On Wed, Aug 31, 2016 at 11:41 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> I am not 100% positive about this but you can try to write Python script
> >> and run parmed (python my.py)
> >>
> >> $ cat my.py
> >>
> >> import parmed as pmd
> >> parm = pmd.load_file("old.parm7")
> >> # suppose your H is 1st atom
> >> atom = parm.atoms[0]
> >> # add you stuff here
> >> atom.name =
> >> atom.type =
> >> atom.atomic_number =
> >> atom.charge =
> >> parm.save('new.parm7')
> >>
> >
> > You also need to change the mass.
> >
> > atom.mass =
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
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Received on Thu Sep 01 2016 - 02:00:03 PDT
