VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Jan 23 2008 - 04:21:01 CST

That's an interesting point, Axel...

> ciao francesco,
>
> ...and i would like to have a tcl script that writes grant proposals
> and if possible, successful ones. ;-)

If you can get TCL scripting working for grant proposal writing,
please let us know! :))

>
> if you want anything this specific and flexible, you're most likely stuck
> writing it yourself. there is a remote chance somebody has written
> something similar and you can adapt it.
>
> ...and then, of course, there is the problem, that (too?) many people don't
> submit their scripts or script fragments to the VMD script library, so a lot
> of useful stuff is lost when they move on to other projects.

That is true. This could happen, in part, because we think that our
lousy scripts are too simple or too specific and wouldn't be useful
for other people. We also assume that there are other people who can
do a better job at writing useful scripts, yet clean and elegant...

>
> other than that, there is also the alternative of sponsoring somebody
> with the proper expertise to write a custom script. since people spend
> a lot of money on computers and (commercial) software, i am always
> wondering why there is nobody offering 'incentives' to get their specific
> problem solved (by and expert and quickly).

this is because... Science is selfless and altruistic! :)

Seriously, I thought the same myself. For example, I consider myself a
bad (really bad sometimes) programmer, so I usually find myself
spending a couple of hours trying to write a simple script. This is a
huge waste of time. Unfortunately, I'm not really sure if there are
people out there who want to deal with these issues in a regular basis
(even when getting incentives!). This might be in part because most of
the people here want to focus on the science and get their work done
(very valid thing to do). And the talented TCL-script writers (like
you or John) are just too busy with many other things!

Cheers,
Michel

>
> i'd be very interested to learn how people here on this mailing list
> see the perspective of having their technical problems sort of
> 'contracted out' so they can focus on the science...
>
> cheers,
> axel.
>
>
> >
> > In doing that from prmtop/mdcrd (I am working with Amber in this moment) I
> > guess that atoms names should be read from a pbd generated from prmtop/mdcrd,
> > and given to the script in their precise format (I mean, for example, that atom
> > names in ff99SB for the protein are uppercase, while those for the ligand in
> > GAFF ff are lowercase).
> >
> > That applies also to Luis Gracia's RMSD Traj Tool that I am finding extremely
> > useful and time saving.
> >
> > Thanks
> > francesco pietra
> >
> >
> > ____________________________________________________________________________________
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> >
>
>
> --
> =======================================================================
> 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.
>