AMBER Archive (2005)

Subject: AMBER: pH=1 MD simulation

From: Harianto Tjong (harianto_at_mailer.sb.fsu.edu)
Date: Tue Nov 15 2005 - 16:16:12 CST

  Dear All,
  I am interested in a simulation of a small peptide or protein in
explicit water under the condition corresponding to pH=1.
  What I want to know is how to assign the partial charge of H atom which
will be attached to the O atom of COO at C-terminus and how to adjust the
partial charges of atoms in the residue at C-terminus.
Or do you have any suggestions regarding pH=1 explicit water simulation ?
  Thank you in advance.
Regards,
Harianto.
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