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PostPosted: Mon Oct 26, 2015 12:24 pm 
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Micromolar User
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Joined: Tue Jan 15, 2013 9:30 am
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After a docking simulation in Autodock 4, one gets this kind of output:


USER RMSD from reference structure = 0.228 A
USER
USER Estimated Free Energy of Binding = -10.77 kcal/mol [=(1)+(2)+(3)-(4)]
USER Estimated Inhibition Constant, Ki = 12.74 nM (nanomolar) [Temperature = 298.15 K]
USER
USER (1) Final Intermolecular Energy = -13.75 kcal/mol
USER vdW + Hbond + desolv Energy = -12.27 kcal/mol
USER Electrostatic Energy = -1.48 kcal/mol
USER (2) Final Total Internal Energy = +0.00 kcal/mol
USER (3) Torsional Free Energy = +2.98 kcal/mol
USER (4) Unbound System's Energy [=(2)] = +0.00 kcal/mol


I would like to decompose the sum from

USER vdW + Hbond + desolv Energy = -12.27 kcal/mol

into their specific terms and get the energetic contributions:

vdW = ..... kcal/mol
Hbond = .... kcal/mol
desol Energy = ... kcal/mol

In addition, I would like to get that information in a per-atom basis. I mean, what is the value of:

vdW for atom1, vdW for atom2, ...., vdW for atom N
Hbond for atom1, Hbond for atom2, ...., Hbond for atom N
desol Energy for atom1, desol Energy for atom2, ...., desol Energy for atom N

What we have tried up to now is to look at the source code. There, and in the file "write pdbqt.cc" there is a structure called "energycomponent". But this is very confusing, since we calculate hbonds per atom and even for carbon atoms, it takes always negative values.

Anybody can help here?

Thanks


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PostPosted: Mon Mar 14, 2016 6:29 pm 
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Millimolar User
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Joined: Tue Mar 03, 2015 1:46 am
Posts: 5
Hi, for the second question, try to look in the .dlg file, where there are the coordinates of the obtained poses (right after the clustering section). It should gove you the vdw and electrostatic energies for each atom, not for the desolvation though.


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