Re: [AMBER] changing atom type

From: Hai Nguyen <>
Date: Wed, 31 Aug 2016 11:41:22 -0400

I am not 100% positive about this but you can try to write Python script
and run parmed (python

$ cat

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.type =
atom.atomic_number =
atom.charge ='new.parm7')

# more info about Atom:

make sure to double-check your saved parm


On Wed, Aug 31, 2016 at 11:16 AM, Jacopo Sgrignani <>

> 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
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Received on Wed Aug 31 2016 - 09:00:03 PDT
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