VMD-L Mailing List

From: Luis Agullo (LAB) (lab_at_lagullo.com)
Date: Tue Nov 03 2009 - 04:50:55 CST

Hello,

I use the functions of autopsfgen, solvation and ionization to prepare
proteins for NAMD. However, I would like to change the charge of specific
amino acids in my protein as estimated by other programs (Propka,...). I
tried to do it with Molefacture, deleting or adding protons to the
structure (the output of autopsfgen); but, after using the other functions
(solvation, ionization), VMD delete those changes and I obtain finally the
initial ionization pattern of my protein. How can I solve that?

Luis