I don't think ParmED HMR will work with PSF or PDB input (if they don't
have atomi_number information for ParmEd).
In general, you can access any ParmEd's Action API by
import parmed as pmd
parm = pmd.load_file('your.prmtop')
pmd.tools.actions.XXXX(parm, arg_list).execute()
(replace XXXX by something like: HMassRepartition)
I suggesst to use IPython to explore its (ParmEd) functions.
Hai
On Fri, Dec 9, 2016 at 10:59 AM, Brian Radak <brian.radak.accts.gmail.com>
wrote:
> Hello,
>
> Is there a simple workflow for using ParmEd to apply hydrogen mass
> repartitioning on PSF/PDB inputs? I gather that this can be done through
> the Python interface, but I can't figure out how to utilize the
> HMassRepartition action in that context.
>
> Thanks,
> Brian
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak.anl.gov
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Received on Fri Dec 09 2016 - 09:30:02 PST
