Potential Energy Calculations
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 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
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
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
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Nikolay, There are a lot of levels to this question -- I hesitate to get into it, because it could be very complicated (and it's not a Chimera question per se). Concerns are why you want to calculate this quantity and whether it has any physical meaning. If you are trying to calculate a solvation energy, there are many well-established computational approaches involving MD or MC simulations, or continuum dielectric calculations. What you describe is only for a single configuration, without sampling or entropy considerations. I would recommend thinking carefully about what quantity you are calculating, how it relates to any real property, and then investigating in the literature (or computational chemistry textbooks), on the web, and by questions to email lists such as CCL how best to proceed in terms of calculations. Probably to get helpful answers from email lists, you should give some rationale, and solicit suggestions about your strategy as well as what programs to use to execute that strategy. Best, 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 8:33 PM, Nikolay Igorovich Rodionov wrote:
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
I recognize that the approach is limited in that scope but I am working with a highly stable macro protein structure and I am not expecting any immense configurational changes when I study the system in MD. I simply trying to redefine the surface of the molecule based on the extent of solvent interaction within the macrostructure. I feel as though an analysis of a generalized energy minimal state will give me a good approximation of how deep interactions persist and give me a better idea of the "surface" atoms than MSMS analysis which simply accounts for VDW size and not VDW interactions per say. The structure is tubular so I was going to create multiple analysis states with atomic cutoffs at varying distances from the center of the energy minimized structure and then compare the relative energies of the systems as I described before. 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 9/22/12 1:38 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Nikolay, There are a lot of levels to this question -- I hesitate to get into it, because it could be very complicated (and it's not a Chimera question per se).
Concerns are why you want to calculate this quantity and whether it has any physical meaning. If you are trying to calculate a solvation energy, there are many well-established computational approaches involving MD or MC simulations, or continuum dielectric calculations. What you describe is only for a single configuration, without sampling or entropy considerations.
I would recommend thinking carefully about what quantity you are calculating, how it relates to any real property, and then investigating in the literature (or computational chemistry textbooks), on the web, and by questions to email lists such as CCL how best to proceed in terms of calculations. Probably to get helpful answers from email lists, you should give some rationale, and solicit suggestions about your strategy as well as what programs to use to execute that strategy. Best, 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 8:33 PM, Nikolay Igorovich Rodionov wrote:
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
participants (2)
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Elaine Meng -
Nikolay Igorovich Rodionov