Oh, you are both right and wrong.
>>> parm = parmed.load_file('my.psf')
is totally valid, but I had no idea about the (undocumented?) trick of
>>> parmed.tools.actions.XXX(parm, arg_list).execute()
Thanks!
Brian
On Fri, Dec 9, 2016 at 11:07 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> > _______________________________________________
> > 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
>
--
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 - 09:30:03 PST
