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Unless you have multiple events of binding and unbinding you cannot
directly calculate the Ki from EM or MD. You can use approximated
methods, e.g. LIE and MM/PBSA (with MD) or LIECE (for a static
structure). All of these depend on the choice of empirical parameters.
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Best regards,<br>
Ran.<br>
<br>
V. Tanchuk wrote:
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<div><font face="Arial" size="3">Dear Users,</font></div>
<div><font size="3"><font face="Arial"> I amworking Drug – Enzyme
Complex. Unfortunately, docking software (AutoDock) was not able to
give any resonable results. I have tried to use Gromacs and got a
resonable binding. The best results were obtained in the case of simple
minimization of the crude AutoDock's results. The question is how to
estimate Ki. </font></font></div>
<div><font size="3"><font face="Arial"> There is also another
problem. I have the best correlation between experimental and
calculated results only for the total energy in the case of
optimization (it seems that other kids of energy are not available
without molecular dynamics, but total or any other energies obtained
after molecular dynamics do not correlate).</font></font></div>
<div></div>
<div><font face="Arial" size="3">Thank you in advance for your help.</font></div>
<div></div>
<div><font size="3">Sincerely yours,</font></div>
<div><font size="3">V. Tanchuk</font></div>
</font></div>
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