Molprobity has a great tool for this under the section Visualize interface contacts. One caveat though, if the small molecule isn't already in ligand depot you have to provide your own PDB format description.
On 2/27/07, mathias <[EMAIL PROTECTED]> wrote:
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
