Is environment PH simulation the better one or is protonated protein PKa simulation better for acid protein?

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Pruthvi Raj Bejugam

Dear Kannan anna, Yes, even i have faced this problem some time back. in that case i have protonated the HIS, ARG, LYS and deprotonated the TYR, CYS residues which was pointed out by Prof. Tarik Nasser. I have used the Pka values given by the protein preparation wizard of Schrodinger maestro software. Accordingly i have prepared the system and then performed the MD simulation

Kannan M.

Thanks for your comments

i will follow accordingly