Subject: RE: CCL:GROMACS and Energy Minimization

From: "Sergio Manzetti" <[email-masked]>
Date: Tue, 28 Aug 2001 22:42:44 -0700

Hi and thanks for all help. I am though very curious about one thing in
GROMACS. When simulationg dimers in water, in the cases with
inhibitors/substrates the non-covalent binding forces between the two chains
might not be favourable. In this case, the reasonable result would be a
slight (or strong) dissociation in vitro. The constraint parameters in the
parameter file in GROMACS make this dissosiation impossible as far as I have
understood, and the mdrun script, when runned constraints will not allow
such dissociation (I presume). In this case, the energy will be the only
reliable factor to deduce something about a enzyme and substrate complex. If
I add constraint parameters in the *mdp file, the chains will probably be
held together anyway, but the mdrun stops because of unusual bond lengths
and violated constratints.
What I would like to know, is HOW should I set the parameters to make this
dissociation possible (if possible in GROMACS?), and finalize the molecular
simulation with graphical and visual data.

Thank you all

Sergio

____________________________________________________________________________
___________________________

Sergio Manzetti
Research Scholar
Centre of Molecular Biotechnology/ Supercomputer Facility
Queensland University of Technology
2 George St.
BRISBANE
4000 QLD
AUSTRALIA
email: [email-masked]
Tlf: +61 7 3864 1434
www:  http://www.life.sci.qut.edu.au/html/research/cmgenetics.html
www2: http://www.its.qut.edu.au/hpc/

-----Original Message-----
From: Bernd Rupp [mailto:[email-masked]]
Sent: Tuesday, August 28, 2001 2:34 AM
To: Sergio Manzetti
Subject: Re: CCL:GROMACS and Energy Minimization

Hi Sergio,

here is an example file, with wich i have calculated insulin dimers(also
more
chains).
hopefully it runs also on you machine.

if you have more questions, you can ask me; but i am also only an user.!?
;-))

what GROMACS version runs on you machine and wich kind of machines do you
have.

chiao

Bernd

--
Bernd Rupp

Heinrich-Heine-Universitaet Duesseldorf	| Gebaeude 26.23  Raum O2.33
Institut fuer Pharmazeutische Chemie    | Tel.: 0211 / 81 - 1 38 27
Universitaetsstr. 1                     | Fax.: 0211 / 81 - 1 38 47
40225 Duesseldorf                       | E-Mail:
[email-masked]