[gmx-users] More ATP TOPOLOGIES

[Raj Badhan]

Dear All
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.

Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.