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@syr.edu On 9/21/12 8:41 PM, "Elaine Meng" <meng@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@syr.edu
On 9/21/12 8:23 PM, "Elaine Meng" <meng@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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