visual approach to construction of QMMM input

[Peter]

Hello Teodoro!

Thank you for your interest : )

> do you think would it be easily feasible
> to have a full applet (with input field structure parsed from an
> up-2-date xml cp2k input tree) in order to allow the creation of the
> whole CP2K input graphically?

Well, it is definitely possible and probably not very hard to
implement. But do you think it will be easier to find some parameter
input field in GUI than write it in plain text? Especially considering
the number of  parameters...
I had some experience with GAMESS graphical input generators and IMHO
they are useless. But I'm definitely a "command shell guy" : )
Anyway, I would participate in integration of CP2K and PyMol with
great pleasure.

Peter

On Apr 21, 6:55 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> Hi Peter,
>
> thanks for posting this useful info!
> I'm pretty sure this will be definitely useful.
>
> I have a feature request! :-p
>
> Im not an expert of pymol, but do you think would it be easily feasible
> to have a full applet (with input field structure parsed from an
> up-2-date xml cp2k input tree) in order to allow the creation of the
> whole CP2K input graphically?
> This, combined with the graphical handling of the molecular system, may
> be really an interesting feature.
>
> I'm ready to bet that this would have even more appeal ;-)
> Teo
>
> Peter wrote:
> > Dear CP2K users,
>
> > Recently I've written a simple script, which could be helpful to those
> > of us, who deals with large QMMM systems.
> > The script is intended to be used from PyMol (http://www.pymol.org/)
> > molecular visualization system and allows one to generate &QM_KIND,
> > &LINK and &CELL parts of CP2K input easily. Given a molecular object
> > name and QM part selection name (which can be defined using either
> > approach available in PyMol) it generates output file with
> > corresponding input groups.
> > To use the script:
> >   1. Download it (http://groups.google.com/group/cp2k/web/gen-cp2k-
> > qmmm.py)
> >   2. Start PyMol and issue the following command from it's shell:
> >      >  run /path/to/script.py
> >   3. Use it:
> >     > gen_cp2k_qmmm filename, qm_part_selection_name,
> > the_whole_system_object
> > The output will be saved to file "filename".
> > N.B.: The file will be overwritten!
>
> > Another PyMol script which you may find handy is a multiframe XYZ file
> > (trajectory) loader (http://groups.google.com/group/cp2k/web/
> > load_xyz_traj.py).
> > "Installation procedure" is pretty the same.
> > Usage:
> >  > load_xyz_traj file.xyz, target_object [, stride]
>
> > N.B.: By default PyMol reorders atoms on molecule load. This PyMol
> > behavior may prevent correct loading of XYZ trajectories. To
> > workaround this issue add the following lines to ~/.pymolrc file
> > (create it if needed):
> > set retain_order, 1
> > set pdb_retain_ids, 1
>
> > Hopefully these simple scripts will help people familiar with PyMol in
> > doing biostuff with CP2K.
>
> > Best regards,
> > Peter