On Mon, Sep 14, 2015 at 11:50 AM, Mykola Dimura <dimura.mykola.gmail.com>
wrote:
> Dear AMBER community,
> I have a problem loading an Amber topology file which contains
> custom-made dummy atoms into parmed.py. I'm using dummy atoms to
> indirectly pull on the groups of atoms, connecting the dummy atom to
> the molecule with NMR restraints.
> So I created frcmod and lib files (see below) and use them to make
> topologies with leap. Obtained topologies work well with pmemd.
> However, when I try to load such a topology with Parmed.py, I get an
> error:
> #####
> ParmEd: a Parameter file Editor
> Traceback (most recent call last):
> File "/home/user/opt/amber14/bin/parmed.py", line 126, in <module>
> amber_prmtop.add_parm(parm)
> File
> "/home/user/opt/amber14/lib/python2.7/site-packages/ParmedTools/parmlist.py",
> line 38, in add_parm
> raise ParmError('Added parm must be Structure or a subclass')
> ParmedTools.exceptions.ParmError: Added parm must be Structure or a
> subclass
> #####
>
>
> Is it possible to load topology with pseudo atoms into Parmed?
>
Yes, it should be fine. Are you sure you're not accidentally giving a
coordinate file name as a prmtop, perhaps?
What command and input are you using?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 14 2015 - 09:30:07 PDT
