[Chimera-users] Potential Energy Calculations

[Nikolay Igorovich Rodionov]

Okay will do, thanks for the advice!


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 8:41 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

>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.
>Best,
>Elaine
>
>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?
>> 
>> Thanks!
>> 
>> 
>> 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
>>> -----
>>> 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
>>> 
>>> 
>> 
>> 
>> 
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>
>