Previous Thread
Next Thread
Print Thread
#34272 08/12/14 08:26 AM
Joined: Aug 2013
Posts: 41
Y
Forum Member
OP Offline
Forum Member
Y
Joined: Aug 2013
Posts: 41
Hi, I have get the trajectory of the MD simulaation,I want to compute the binding free energy between protein and ligand, how to do it?
Thanks!

Joined: Sep 2003
Posts: 4,840
Likes: 3
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,840
Likes: 3
This does not seem to be a question concerning any of the examples in this forum.

The most reliable methods to compute free energies require a special simulation ("free-energy perturbation","thermodynamic integration","potential of mean force") and are not used with a standard trajectory.
Your question should have been asked BEFORE you started your simulations.

MM-PB/SA (or variants) can be used, but may be of lesser quality. The LIE method of Johan Åqvist is another possibility, but you still have to have a trajectory of the free ligand, and you should check for convergence of your results in all cases.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.007s Queries: 18 (0.004s) Memory: 0.7272 MB (Peak: 0.7676 MB) Data Comp: Off Server Time: 2022-08-16 12:31:39 UTC
Valid HTML 5 and Valid CSS