[AMBER] The interaction energy between substrate molecule and protein

Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Meng Wu <wumeng.shanghaitech.edu.cn>
Date: Thu, 22 Nov 2018 10:44:55 +0000

Dear all,

I have finished running the MD simulations of an ion channel protein, now I want to calculate the interaction energy between the substrate molecule and protein from the trajctories. I have tried "lie" command in cpptraj, but the result is so large especially the electrostatic terms, this may be due to my substrate molecule is charged. I wander is there other way to calculate the interaction energy in my case? Thank you in advance!

All the best,
Meng Wu

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 22 2018 - 03:00:02 PST