[gmx-users] More ATP TOPOLOGIES
r.k.badhan at stud.man.ac.uk
Tue Dec 16 22:27:01 CET 2003
Sorry to bug you all again.
I am still having trouble with this ATP thing.
My system is a dimer with ATP docking in the active site in
between the dimer. When I editconf a box or genbox this, the
ligand breaks. I then tried this with a very similar "real" structure (
my system is a relatively "correct" homology model), and the same
thing happen with this too.
However, I can editconf a box and genbox etc the ATP on its own
without the protein.
So, I guess it comes down to either bad contacts (which I have
checked and corrected for both in SwissPDB) or ATP topology.
I thought that the ATP topology may be wrong, as many have
suggested, but how could this in itself lead to ATP becoming
distorted and stretched when I editconf and create a box?
It seems strange and is indeed a stumbling block at the moment.
School of Pharmacy and Pharmacetical Science
The University of Manchester
More information about the gromacs.org_gmx-users