Free Energy Calculation: State B has non-zero total charge: -1.000000

pmx
1

Dear Bioexcel Community
I need your suggestions regarding the following problem:-
I am trying to calculate the free energy of mutating from Arginine to Histidine residue in a protein. I have prepared the system using pmx tools
http://pmx.mpibpc.mpg.de/janssen_tutorial_peptide/index.html
I have neutralized the system however during the grompp I get the following error:-

“State B has non-zero total charge: -1.000000”
Could you please suggest to me how should I set state B to zero charge without affecting the charge of state A?

Thanks in advance.
Sadaf

2

There are several ways to deal with this:
a) simulate charged system and later correct dG for that
b) retain the constant neutral charge of the simulation box. For that you could construct a single-system/double-box setup: Figure 3 in this book chapter http://www3.mpibpc.mpg.de/groups/de_groot/pdf/Gapsys_MolMod_2015.pdf

Vytas