[Chimera-users] Potential Energy Calculations

Nikolay Igorovich Rodionov nirodion at syr.edu
Sat Sep 22 11:02:02 PDT 2012

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 at syr.edu

On 9/22/12 1:38 PM, "Elaine Meng" <meng at 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
>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
>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.
>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
>> 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,
>> 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
>> the protein & water system, shouldn't this leave me with just
>> 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
>> 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

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