metal nano particle and protein

[Hamid Mosaddeghi]

Hi

I want to calculate binding energy between protein and metal nano particle. metal nanoparticle is fixed and not movable (non bonded interaction considered).

I ran g_mmpbsa code but I get "NaN" number, why? this error come back to unmovable metal nano particle?  

thanks in advance

[idris mukhtar]

Hi!

I am not sure I have a solution to this because I haven't worked on metal nanoparticles. Btw, If I understood your question well, it should be similar to this in below link

https://www.researchgate.net/post/Why_Gromacs_mmpbsa_shows_nan_in_energy_values 

 

To know the cause, maybe the below link can tell you why you get "nan".

http://archive.ambermd.org/201205/0649.html 

http://archive.ambermd.org/201408/0392.html  


I hope this helps.

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Mukhtar Oluwaseun IDRIS

School of LifeSciences,

University of Science and Technology of China Hefei, China.

Tel: +86-13295516623