I am using 1BRS (barnase-barstar) for binding energy calculation using g_mmpbsa. Generally i remove water from the md simulation trajectory and then use trajectory, topology and index file for binding energy calculation. I have got -560.62kj/mol, -292.123kj/mol and -172.451kj/mol for using 2 , 3 and 4 dielectric constant respectively.
now I have confusion that is it necessary to remove water from trajectory?
Basically, the mmPBSA is designed to use the implicit water model to calculate the solvent energy which could not be evaluated through the explicit model because of the huge energy fluctuation of the explicit water. So, there is nothing wrong of removing the water from the trajectory. But I don't know whether the program could automatically eliminate the water if the water is in the input file.
You can remove water molecules with parmed if you are using amber topology files.
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