From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Jul 06 2009 - 05:17:30 CDT

Axel,

Thanks. It worked when the executable was included in path. By default, it
would be nice too (at least in Linux) if it worked when both the namd and
the vmd executables were in the same location.

Please let know if you worked out the -exe flag option.

Regards,
Neela

On Mon, Jul 6, 2009 at 12:28 AM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> wrote:

> 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.
>
>