[gmx-users] how to obtain binding energy?

Justin A. Lemkul jalemkul at vt.edu
Wed May 18 13:28:09 CEST 2011

shahab shariati wrote:
> Dear Justin
> thanks for your time and attention
> in address 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
> in Tutorial 3: Umbrella Sampling 
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html>, 
> in Step One, you said '' For protein-ligand systems, please consult this 
> tutorial 
> <http://eugen.leitl.org/chem/kerrigje/pdf_files/trp_drug_tutor.pdf> ''.
> unfortunately, I can't access that (when clicked on link: Apologies, but 
> the page you requested could not be found).
> how to access to that link?

The page must have moved.  Please refer to 

> I have another question about my system (protein-dna complex). If I do a 
> mutation in protein, can I obtain delta delta G by PMF method again?

I would suggest you consult my paper that is associated with the umbrella 
sampling tutorial.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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