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PostPosted: Mon May 07, 2012 11:52 am 
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Joined: Mon May 07, 2012 11:12 am
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I have docked a number of ligands with my protein of interest and have generated a PDB file of the protein plus the docked ligand.
However when I try to open the PDB file in ligand explorer, the system appears to stall.
I believe that the main problem is the labeling of atoms for the docked ligand.
I was wondering if anybody has any suggestions to deal with this problem.

Also, I have tried to create a list of interactions (with distances, types of interactions etc) in Autodock .
However I have only been able to create a short list of close contacts and hydrogen bond interactions.
Does anybody know how to create a more comprehensive list of the protein-ligand interactions in Autodock 4.0?

Cheers,
Ray.


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PostPosted: Wed May 30, 2012 9:54 am 
What do you mean by "more comprehensive"?


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PostPosted: Fri Jun 01, 2012 9:45 am 
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Joined: Mon May 07, 2012 11:12 am
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I would like a more detailed description of the interactions.
When analyzing interactions in Autodock, the program gives
a list of hydrogen bonds interactions and close contacts.

I would like to get a detailed list, which describes the
hydrogen bonds (atoms involved and distances) and
hydrophobic interactions (the same, atoms and distances).
This is done in ligand explorer, however I am unable to get the
same detail in autodock

Cheers
Ray.


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