On Fri, Dec 9, 2016 at 12:28 PM, Brian Radak <brian.radak.accts.gmail.com>
wrote:
> ParmEd can't infer atomic numbers based on mass or atom names?
>
>
It does but I don't think this apply for all formats.
PSF
In [4]: parm = pmd.load_file('ala3.psf')
In [5]: [atom for atom in parm.atoms if atom.atomic_number == 1]
Out[5]: []
PDB is ok
In [6]: parm = pmd.load_file('1L2Y.pdb')
In [7]: [atom for atom in parm.atoms if atom.atomic_number == 1][:3]
Out[7]: [<Atom H1 [8]; In ASN 0>, <Atom H2 [9]; In ASN 0>, <Atom H3 [10];
In ASN 0>]
I already open an issue here: https://github.com/ParmEd/ParmEd/issues/798
Hai
> On Fri, Dec 9, 2016 at 11:25 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > On Fri, Dec 9, 2016 at 12:18 PM, Brian Radak <
> brian.radak.accts.gmail.com>
> > wrote:
> >
> > > Oh, you are both right and wrong.
> > >
> > >
> > I talked about atomic_number and HMR, I did not say anything about
> > "load_file".
> > If you do not provide correct atomic number for your psf, you can't do
> HMR.
> >
> >
> >
> > > >>> parm = parmed.load_file('my.psf')
> > >
> > > is totally valid, but I had no idea about the (undocumented?) trick of
> > >
> > >
> > there is no trick. The document is in ParmEd's website:
> > https://parmed.github.io/ParmEd/html/parmed_api.html
> >
> > Hai
> >
> > >>> 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
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> > >
> > >
> > >
> > > --
> > > 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
> > >
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
>
>
>
> --
> 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
>
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Received on Fri Dec 09 2016 - 10:00:02 PST
