[gmx-users] more questions

[Daan van Aalten]

Hi Anton

Sure, but before that happens it needs to be tested a bit more. I haven;t
actually heard of *anyone* (!) simulating a PRODRGged small molecule in
GMX with success. That could mean lots of people have tried and it works
perfectly or nobody has tried because it doesn;t work :-) 
(so if YOU out there have tried and failed/succeeded, let me know!)
Once these small things work OK we can move onto entire proteins.

cheers

Daan

On Tue, 9 Oct 2001, K.A.Feenstra wrote:

> David van der Spoel wrote:
> > 
> > On Tue, 9 Oct 2001, Daan van Aalten wrote:
> > >
> > >Once the size limit on PRODRG is gone, one should be able to build entire
> > >topologies for protein which contain as much of these modifications as you
> > >want. Perhaps you can test a small section of your protein (< 100 atoms)
> > >with this chromophore in the middle? If it works I'll try to free some
> > >time to up the size limit to 10000 or so.
> > 
> > Obviously most users would really welcome this. Hope your algorithm scales
> > reasonably.
> 
> And if it really works well, we should consider it as a replacement
> for pdb2gmx, maybe for GROMACS 4.0... :) Or maybe, to use it as a
> starting point for a complete re-write of pdb2gmx, which we would need
> to do at some time anyway... ;)
> That is, if Daan also thinks that would be a good idea?
> 
> 
> -- 
> Groetjes,
> 
> Anton
>  _____________ _____________________________________________________
> |             |                                                     |
> |  _   _  ___,| Anton Feenstra        Dept. of Biophysical Chemistry|
> | / \ / \'| | | anton at chem.rug.nl            University of Groningen|
> |(   |   )| | | +31 50 363 4327      Nijenborgh 4  9747 AG Groningen|
> | \_/ \_/ | | | http://md.chem.rug.nl/~anton         The Netherlands|
> |             | "Microsecond Here I Come" (P.J. Van Maaren)         |
> |_____________|_____________________________________________________|
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
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