[Chimera-users] Potential Energy Calculations

Nikolay Igorovich Rodionov nirodion at syr.edu
Fri Sep 21 17:30:32 PDT 2012

Would it be make sense to compute the total energy for the protein w/o
water and then loaded with water, and then take the difference to be
energy due to interaction?


Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015
Martin J. Whitman School of Management & L.C. Smith College of Engineering
at Syracuse University

Syracuse, New York 13244
Phone: 281.301.9401| Email: Nirodion at syr.edu

On 9/21/12 8:23 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

>Hi Nikolay,
>Sorry, no.  Although the minimizer reports an energy, it is the total
>energy of the system, and no breakdown is available.
>Elaine C. Meng, Ph.D.
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote:
>> Hi all, 
>> I was wondering the there is a tool in chimera that can find the net
>>interaction potential energy between models, something like Lennard
>>Jones Potential. Specifically, I need to measure the interaction
>>potential between a protein and water in a solvated system.
>> Thanks! 
>> Nikolay Rodionov

More information about the Chimera-users mailing list