Ionization with VMD

From: Luis Agullo (LAB) (
Date: Thu Oct 15 2009 - 09:07:13 CDT

Maybe, it is not the forum... I am using Solvation and Ionization
extensions of VMD to prepare proteins before simulation with NAMD. When
Ionization is done selecting the 'Neutralization' option, the program
calculates protein charge. This estimation is similar, but not identical,
to the values obtained with other programs. Two questions about that:
    1. How does VMD calculate this value?
    2. Is it possible to set 'a custom' protein charge (estimated by
another software) in this ionization extension of VMD?


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