Thermodynamic integration question

From: Randall Hall (
Date: Sat Sep 05 2015 - 23:28:57 CDT

Dear List Members,
  Is there a sample pdb input file for a thermodynamic integration? If not, my question is related to the structure of the pdb file. If I understand the documentation, if I wish to mutate LYS to ARG, for example, I need to create a new residue that has two side chains attached to the same NH-CH-CO backbone structure. Is this correct?


Randall Hall
Lillian L.Y. Wang Yin, Ph.D. Endowed Professor of Chemistry
Chair, Department of Natural Sciences and Mathematics
Dominican University of California
Phone: 415-482-1911
Fax: 415-482-1972

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