I have a perl script to do this job.
The pdb file should contain your ligand.
Simplest way to run it is "lig_contact file.pdb"
If the script does not find the ligand, you can switch to command line options.
The script prepares a pymol input file and fires it up to display the interactions.
After you close the pymol window you can see the pymol script file. The list of interactions is listed as "distance .?? = (ligand atom), (protein atom)." in this file. The '??' could be cc (hydrophobic interaction) or hb (hydrogen bond).
Thanks
Abhinav
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of mathias
Sent: Tuesday, February 27, 2007 10:44 AM
To: [log in to unmask]
Subject: [ccp4bb] software to calculate VDW interactions between small molecule and protein
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
binding to protein. The only information I need is an output file
which lists all amino acids of the target protein which make VDW
interactions with the binding small molecule.
Thank you very much for your help and recommendations,
Mathias
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