Re: [Apbs-users] atom # is off the mesh (ignoring) ERROR

[Nathan B. <ba...@bi...>]

Hi Pinar --

Gernot is right; these molecules need to be aligned.  However, in order to
use the electrostatic energy calculation method you're describing, these
molecules need to be *perfectly* aligned since you're relying on this
alignment to cancel self-interaction energies.  Please be sure to check that
the atoms are in the same locations after alignment.

Thanks,

Nathan

On Fri, Nov 21, 2008 at 6:25 AM, Gernot Kieseritzky <
ge...@ch...> wrote:

> Hi!
>
> On Fri, 2008-11-21 at 12:02 +0200, Pinar KANLIKILICER wrote:
> >
> > 0.pqr is the complex (molecule1). I constructed these files according
> > to the results of molecular dynamic simulations. PDB files (which were
> > used in pdb2pqr web server) are the snaphots which were extracted from
> > MD simulations belonging to protein1,protein2 and complex
> > simulations,separately. So coordinates are not the same in all PDB
> > files.
>
> So just before you generate PQR files, just run the Kabsch algorithm on
> your snapshots from the monomer MD, i.e. align the monomor coordinates
> on the dimer structure.
>
> Greetings,
> Gernot
>
>


-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/