[gmx-users] query regarding coming out of ligand from protein during simulation

[Justin A. Lemkul]

sangeeta kundu wrote:
> Dear all,
> 
>  
> 
>  
> 
>  
> 
>     I am trying to perform simulation of a protein with several ligands, 
> in case of certain ligands I found that the ligand  is coming out of the 
> protein after 5-6 ns. I have checked the energy of the system, but it 
> does not show any abrupt change, still the ligand is coming out of 
> protein after a certain time.Is it due to steric hindrance during the 
> course of the simulation or something else?   I can not debug, please 
> help. Thanks in advance.
> 
>  
> 

Several possibilities:

1. You have lousy parameters for your ligand.
2. Periodicity effects (search the archive).
3. The ligand doesn't bind strongly, so this is normal.

#1 and #2 are the most likely, given the time scale you've used.

-Justin

>  
> 
> regards
> 
> Sangeeta
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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