[gmx-users] pdb2gmx on KcsA

[David Mobley]

Modeler is a program that can do this sort of thing (build in missing
residues) from the sequence and structures without the missing residues or
homologous structures.

On 12/28/05, Kaasi Sridhara <research.gromacs at gmail.com> 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".
> >
>
>
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