[gmx-users] TI results

[Justin A. Lemkul]

parto haghighi wrote:
> Dear GMX users,
> I want to prepare an .itp for a new molecule ( like fifth gromacs tutorial).
> 1 ) I applied PRODRG to create its drg.itp.
> 2 ) Now I want to correct its partial atomic charge.
> 
> As I have red in a paper (http://pubs.acs.org/doi/abs/10.1021/ci100335w) 
> I have to do thermodynamic integration for example solvation free energy 
> of this molecule in water to correct its charges.
> The molecule is lidocain
> My question is how can I accept my free energy calculation results while 
> I dont have any experimental date to comparison?
> 

When it becomes clear that the free energy of solvation itself is not a quantity 
to which you can compare, you need something else.  One such option that we have 
used in the past is comparing logP values (see our paper at 
http://pubs.acs.org/doi/abs/10.1021/bi1000855).  For a drug molecule, finding a 
logP value should be trivial ;)

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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