[Chimera-users] Potential Energy Calculations

[Nikolay Igorovich Rodionov]

Hi Elaine, 

I posted my question on the ccl mail server, but I have one more question
for you. I realize that this might be entirely appropriate for this
mailing list but regarding my previous proposal, what if I modify the
method to create 3 files.

One file will be with just the protein, one with the solvated protein, and
one it just the water molecules isolated from the solvated model. If I
calculate the net energy in the each system, and then subtract the net
energies of the protein only and water only systems from the net energy of
the protein & water system, shouldn't this leave me with just interaction
energy?

I was also thinking about putting all of the water molecules into an
energy minima orientation in both files with water by first running the
minimization function in the file with water & protein, and then isolating
the water molecules and writing them into a separate PDB for the
water-only file since the energy minima orientation will change based on
the environment. 

Thanks for pointing me to a great resource by the way.


Nikolay Rodionov


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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>
>