[gmx-users] More ATP TOPOLOGIES

David spoel at xray.bmc.uu.se
Tue Dec 16 22:38:01 CET 2003

On Tue, 2003-12-16 at 22:26, Raj Badhan wrote:
> 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.

So show me where it breaks, and exactly at which step in the process. We
need the complete gro/pdb file before and after running editconf. 

> 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.
neither editconf nor genbox checks for bad contacts in your starting
structure. I suspect that swiss pdb writes out a rotten pdb file.

> 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.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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