[gmx-users] pdb2gmx on KcsA

[Daan van Aalten]

Dear Kaasi & list

A very good solution to the "missing side chain problem" is build into the
molecular modelling program WHAT IF - the command %fixall will do just
that - fix it all. A bit of googling will find you the what if site.

Please note however, that this is not a substitute for checking manually
that everything is OK - my advice would be: don't simulate it if you don;t
understand it!

Daan

On Wed, 28 Dec 2005, Kaasi Sridhara wrote:

> I am unable to find resonable sidechains to be added, as Tsjerk and yourself
> mentioned. I will try to look at the  molecule builder programs available,
> try to see what "reasonable" sidechains can be added, and proceed.
> I am not "that" familiar with biochemistry, as myself being an electrical
> engineer, but working in bioelectrics simulations.
> Thanks for the suggestions, I will get back to you once I do my homework
> properly.
> Thanks again....
>
> >
> > On 12/28/05, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > >
> > > > Did anyone tried to work on this problem earlier, or can anyone
> > > suggest
> > > > how
> > > > to deal with this problem of adding missing residues.
> > >
> > > One approach is to use some visual molecule builder program to pick a
> > > chemically reasonable starting point for each of the side chains you
> > > have
> > > to build and do an energy minimisation on that (preferably restraining
> > > the
> > > atoms you haven't fabricated to their positions in the PDB file). You
> > > would want to be intelligent about side chains in active sites or pores
> > > or
> > > whatever.
> > >
> > > Mark
> > >
> > >
> > > _______________________________________________
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> >
> >
> >
> > --
> > Viswanadham Sridhara,
> > Graduate Research Assistant,
> > Old Dominion University, "VIRGINIA".
> >
>


##############################################################################
Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
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: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk