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 Wed Aug 31 2016 - 14:30:02 PDT
