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writing out the compoments of a molecular complex
#38343 09/09/21 04:07 PM
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Dani Offline OP
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In order to obtain binding energies between two proteins I have run a dynamics of the complex and I would like to extract the component proteins in order to obtain the energy differences.
The script that I generated produces an error for a missing unit number.
I include the input and the ouput file.
Thanks in advance,

Attached Files
error1.zip (16.16 KB, 271 downloads)
SHA1: 5fdca146c3156ad73a58bdbf762d3503a879e174
Re: writing out the compoments of a molecular complex
Dani #38344 09/09/21 11:28 PM
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rmv Online Content
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The input file is corrupted and has garbage text in it, so you'll need to clean it up or get a new copy of the file.


Rick Venable
computational chemist

Re: writing out the compoments of a molecular complex
rmv #38345 09/12/21 02:15 PM
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Dear Dr. Venable,
Thanks for your answer.
Anyhow I would to know if the commands I used in the script to separate the complex into its components are the appropiate ones-
Thanks

Re: writing out the compoments of a molecular complex
Dani #38346 09/12/21 03:51 PM
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It's not completely clear what you're trying to do, and why you want to separate the components. Binding energy can be difficult to compute; getting the potential energy of an interaction is fairly easy in CHARMM, and does not require separating the components. The difficult part is estimating the entropy contribution, the TdS term in the standard free energy expression. Part of the problem is sampling; most simulations are too short to explore a major fraction of the phase space of a binding interaction for two large, flexible molecules.


Rick Venable
computational chemist

Re: writing out the compoments of a molecular complex
Dani #38347 09/13/21 01:36 PM
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I am trying to estimate theses energies without the entropy component as a zero order approximation.

I suppose (in the rigid body approxumation) I could also select the atoms of both proteins and then ask for an interaction energy. This would avoid having to split the system and generating the energy difference a priori.

Re: writing out the compoments of a molecular complex
Dani #38348 09/13/21 05:44 PM
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You'd probably need to run separate simulations of the two proteins isolated from each other, and include the solvation energies in the calculations at the least. Because of the likely conformational changes of surface groups (and more) involved in the binding, the entropy effects could be substantial.


Rick Venable
computational chemist


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