[gmx-users] ParmED

[Qinghua Liao]

Hello,

Here is my script " input.py ":
#
import parmed as pmd

#convert prmtop and inpcrd into top and gro
amber = pmd.load_file('mol_HMR.prmtop','mol_HMR.inpcrd')
#
amber.save('topol.top')
amber.save('ions.gro')
#
system = pmd.load_file('topol.top')
system.write('topol2.top', combine=[[0,1]])
#

You run it as "amber.python input.py ". It works for me well.


All the best,
Qinghua


On 1/14/19 11:05 PM, Hosein Geraili Daronkola wrote:
> Hi everybody,
> I am trying to convert Amber prmtop and inpcrd to gro and top with parmED,
> as in this post
> https://github.com/ParmEd/ParmEd/issues/631.
> But the problem is, ParmED cannot import the pmd. The error is:
> import command is not recognized.
>
> ParmED is working for anything else.
> What can be wrong?
> Best