[gmx-users] query for binding energy

[Justin A. Lemkul]

devawati dutta wrote:
> 
> 
> Dear Sir,
>                I have simulated my protein ligand complex without using 
> PME but with cut-off as  coulombtype parameter. With g_energy command I 
> am getting the value of non-bonded interactions as follows:
> Interaction 	LJ-SR  	    LJ-LR 	   Coul-SR 	    Coul-LR
> P+L(bound) 	-113.2000 	-8.1800 	-15.0650 	6.7500
> L+S(bound) 	-93.4900 	-10.2900 	-18.5400 	-2.2700
> 
> L+S(free)
> 
> 	
> 
> -155.3160
> 
> 	
> 
> -14.0290
> 
> 	
> 
> -31.7500
> 
> 	
> 
> -3.4600
> 
> And I calculated the binding energy through LIE and I got binding 
> energy= -5.17 Kj/mol. I need the value in Kcal/mol. And after converting 
> the valu in Kcal/mol, its a very small value of -1.23 Kcal/mol.I think 
> its not a correct value. Am I getting the right values for the 
> non-bonded Intearctions? Or I should get higher values (for LJ and 
> Coul). I am unable to understand what fault I am doing? Please help me out.
>  

Upon what are you basing the conclusion that the answer is not right?  Is there 
an experimental value that is known?  Or does the result simply not fit what you 
want it to be?

In any case, there are a number of reasons you may not have a correct answer. 
Are your force field parameters correct?  What force field are you using?  How 
long were the simulations?  Have you done replicates, or are you basing the 
result on only a single trajectory of each system?  What was in your .mdp file?

-Justin

> Your's sincerely
> Devawati Dutta
> 

-- 
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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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