[Chimera-users] how to find non-bonded interactions between a protein and a ligand?

Sam Paul D reachsampaul at gmail.com
Thu Jan 22 19:46:33 PST 2015

Hi Elaine,
Thank you so much for all the helpful suggestions.

Sent from my iPhone

> On 22-Jan-2015, at 23:46, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Sam,
> Well, those are the default settings for contacts, so we believe them to be reasonable.  However, "optimal" would be too strong a word, and it surely depends on the resolution of the structure, local B-factors, whether you used docking to generate the complex, etc. As stated in the docs,
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> "For detecting contacts, negative cutoff values of 0.0-(–1.0) Å are recommended along with a hydrogen bond allowance of 0.0 Å. The default contact criteria in the Find Clashes/Contacts graphical interface are –0.4 and 0.0 Å, respectively."
> It is a typical example of setting parameters in computational chemistry.  Software developers try to suggest something reasonable, but it is often the responsibility of the scientist to always pay attention to and critically evaluate the results, and perhaps explore a range of values to see what happens (especially for quick calculations like this).  Often there is NOT one true correct value, and that's one reason they are user-adjustable in the interface.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jan 21, 2015, at 5:50 PM, Sam Paul D <reachsampaul at gmail.com> wrote:
>> Hi Elaine, 
>> First of all thanks for all the suggestions.
>> I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand.
>> Thanks!
>> Sam

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