Hi, I ran a DM simulation of a system with enough ionic concentration to neutralize the system (5 Na added to 1 structural NaCl). Now I want to do an MM-PBSA analysis between protein and ligand but I don't know what concentration of ions to put in the .mdp of g_mmpbsa. Can you help me with this problem?
Mayur Mukhi
Since you added only enough ions to neutralize the charges, your ionic conc. should be 0.00.
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Ricardo J Ferreira
g_mmpbsa ignores the number of ions. Leave the default value in mmpbsa.mdp (pconc = 0.150; nconc = 0.150). You will get this message (NOsh: Deprecated use of ION keyword! Use key-value pairs) and there is no way to correct this.
But the results should be accurate nonetheless.
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