From: Andres Morales N (
Date: Sat Aug 28 2010 - 21:11:49 CDT

Dear VMD users

I need to make simulations of a system at low pH . I found that I should protonate some amino acids to simulate this pH condition. Particularly, I need to equilibrate the loop36 of hemagglutinin at pH of 5.0. The amino acid sequence of this polypeptide is : ARG VAL ILE GLU LYS THR ASN GLU LYS PHE HIS GLN ILE GLU LYS GLU PHE SER GLU VAL GLU GLY ARG ILE GLN ASP LEU GLU LYS TYR VAL GLU ASP THR LYS ILE
I know that I should do the protonation in HIS, but I do not know if I should it with other amino acids. (I work with the polypeptide in a water sphere).
I wait that someone can help me with this.
Thanks for your help.
Andres Morales N.
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253

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