From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Jul 05 2009 - 13:58:50 CDT

On Sun, 2009-07-05 at 12:16 +0530, Neelanjana Sengupta wrote:
> Axel,
>
> I did not realize that NAMDenergy actually looks for the NAMD
> executable:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/

yes, it does. how else should it work?
VMD knows nothing about how to do a simulation.

> How would one specify the path to the executable (if its not present
> in the default location where NAMDenergy looks for it)?

right now, you have to make sure that an executable namd2
is somewhere in your path. namdenergy uses the exetool package
to search the path for an executable called namd2 (or namd2.exe
on windows, if i remember correctly).

i will look into adding an -exe option to manually specify
the location of the namd binary for the script version. that
should be straightforward. adding it to the GUI would be
more complicated and i don't want to do this so close to a
release.

cheers,
  axel.

p.s.: always keep the mailing list in cc when replying.

>
> Thanks a lot for your help!
> -Neela
>
> On Sat, Jul 4, 2009 at 10:24 PM, Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Sat, 2009-07-04 at 21:47 +0530, Neelanjana Sengupta wrote:
> > Dear VMD community,
>
> dear neela,
>
> [...]
>
> > namdEnergy) Running:
> > namdEnergy) namd-temp.namd
>
>
> ^^ the path to your namd executable should be here.
>
> > couldn't execute "": no such file or directory
>
>
> and consequently, "" is not found.
>
> > Info) Finished with coordinate file namd-temp.pdb.
> > Info) Finished with coordinate file namd-temp.pdb.
> > Info) Finished with coordinate file namd-temp.dcd.
> > ===================================
> >
> > I have highlighted the problematic part of the message. I
> tend to
> > think this has more to do with the VMD version than the
> platform
> > (otherwise the temp pdb and dcd files would not even be
> created).
>
>
> ...and i tend to think this has more to do with VMD not
> being able to find your namd binary, or you not giving
> the proper input for that.
>
> in any case, please first check the latest VMD beta version
> and see if the problem persists.
>
> cheers,
> axel.
>
>
> > Any help would be greatly appreciated.
> >
> > Thanks,
> > Neela
> > (Neelanjana Sengupta)
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of
> Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a
> better idiot.
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.