Re: Ionization with VMD

From: Axel Kohlmeyer (
Date: Thu Oct 15 2009 - 09:48:29 CDT


On Thu, Oct 15, 2009 at 10:07 AM, Luis Agullo (LAB) <> wrote:
> Maybe, it is not the forum... I am using Solvation and Ionization

yes, this is not the forum. there is a VMD mailing list. you should
post VMD questions there.

> 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?

from the data you give it, e.g. the charge data in the .psf file.

> 2. Is it possible to set 'a custom' protein charge (estimated by
> another software) in this ionization extension of VMD?

no. the ionization state of your protein is not at all touched by this tool.
it only selects the number of positive or negative ions so that the _total_
system is (almost) neutral.


> Luis

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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