[Chimera-users] Potential Energy Calculations
meng at cgl.ucsf.edu
Fri Sep 21 17:41:19 PDT 2012
In my opinion, no. Maybe you could ask for recommendations of what program(s) would be more appropriate on ccl.net -- we're getting into the territory of general computational chemistry issues that are probably beyond the scope of this forum.
On Sep 21, 2012, at 5:30 PM, Nikolay Igorovich Rodionov wrote:
> 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.
>>> Nikolay Rodionov
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