[gmx-users] pdb2gmx on KcsA
research.gromacs at gmail.com
Wed Dec 28 18:20:07 CET 2005
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
> 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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