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')
# more info about Atom:
http://parmed.github.io/ParmEd/html/topobj/parmed.topologyobjects.Atom.html
make sure to double-check your saved parm
Hai
On Wed, Aug 31, 2016 at 11:16 AM, Jacopo Sgrignani <sgrigna.gmail.com>
wrote:
> Dear all
> I'm doing qm/mm calculations using sander and ORCA.
> I would like to repeat calculations with the same structures but changing
> one atom of the bound small molecole from H to F and the to Br.
> This atom is in the QM zone.
> Is it a simple way to do this without saving a pdb, preparing a new
> molecule library and saving a new prmtop file.
> I had a look to parmed but I think this is not possible with this script.
>
> thanks in advance for your help
>
> Jacopo
>
> Jacopo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 31 2016 - 09:00:03 PDT
