How can I calculate antrophy using gromacs?

Najme Dehghanbanadaki @Najme_Dehghanbanadaki

12 December 2017 1 9K Report

Hello every body

I want to calculate the antrophy amount of a protein-protein complex using gmmpbsa module of gromacs. I can calculate binding energy but not antrophy.

If you have any exprInce,pleas tell me.

Thank you in advance

Najme Dehghanbanadaki

Dear Son Tung Ngo

Thank you for your complete answer.

I calculate the binding energy for a protein-protein complex in water using g_mmpnsa.

Now I have some questions about your answer.

Calculating antropy in vacuum dose not have any matter? It is in cordinance of binding energy calculation in water?

I now how i shoud perform explicit all atom MD. Pleas tell me how can I run an implicit one for my system using gromacs?do you have any toterial?

About normal mode analysis I don't have any experience. Coul you pleas tell me how could I perform it on my system step by step?

Thank you very much in advance

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