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

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fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

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fatal error

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fatal error

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fatal error

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Does the pressure(-600 mmHg) affects pH?

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Ester cleavage conditions?

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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