🚀 go-pugleaf

< call for feasability study deleted>

>
>[Although I do not share Mr. Dunphy's pessimism, I second his proposal
> empahtically... Before we can do this in more than a handwaving
> way, however, we need molecular simulation software.  Does anyone know of
> any usable PD codes,

I believe that the Gromos software of Prof van Gundsteren is free (you might
have to pay for the tape) if not actually PD.  Failing that it's getting
quite difficult to acquire free MD software because companies are now
realizing that a great potential market exists.  Some people are even suddenly
finding that they are no longer permitted access sources that they wrote :-(

(btw MD = Molecular Dynamics, I hope nobody is going to seriously suggest a 
Quantum approach ?)

> or is there any interest in a sci.nanotech-based collaboration to produce
> such a beast?

Count me in.  I'm not sure that it's strictly necessary, however.  If we could
agree on an exchange format it would be easy to knock up a set of conversion
programs to generate whatever format your software required.

> --JoSH]

w.r.t the proposed feasability study, to what tests do we whish to subject
any proposed designs.  As i see it, there are * things to consider:

1) Chemical Legitimacy:  Is the structure actually possible within the laws of
   chemistry.  (Is there an existing expert system that would assess this ?
   Some of the more user friendly MD packages will 'parse ' a potential
   structure and report open valencies etc. but I wouldn't take their word
   as gospell) failing this shgould we appoint a commitee of our more
   'chemical' contributors ?

2) Conformational Stability:  Does the structure dekay into another, more-
   stable conformation when subjected to Energy Minimization and/or MD ?  
   Which force-field do we consider most accurate for this determination ?
   What temperature do we require the structure for withstand, for how long ?

3) Can the proposed structure be readily synthesized ?  This is less 
   important because given a functional but un-makeable device, we could
   probably rework the design until it was plausible.  (As above, is their an
   expert system that can do this.  I know that several of the 'great'
   pharmaceuticals houses have such programs but that they do not admit to
   using them because their is some doubt about the patent/copyright on
   things designed by a machine (in some countries at least).)

4) Does it perform the task claimed, will it do so under simulation?  How
   robust is its behaviour ?

With regard to 2 and 4 is it possible for someone to set up a Dynamics-Server
(not sure whether I could all out machines are heavily used (but we're getting
more>) that would recieve a design in a standard format and subject it to
a standard regiem of Energy Minimisation and Dynamics ?

One other small niggle.  Whenever people have suggested this before, nothing
has happened!  What is it, are you all lazy ?  (Or is it really impossible ?)