AMBER Archive (2007)

Subject: AMBER: thermodynamic integration

From: Servaas Michielssens (servaas.michielssens_at_student.kuleuven.be)
Date: Thu May 24 2007 - 10:50:48 CDT

I was trying to do thermodynamic integration to calculate pKa values
(in amber8). I made a perturbed paramter file in xleap, but I changed
the parameters manual, not by the edit command in leap. I typed the
changed values in the topology file under the flag pert_charge. I
placed the anionic form in pert_charge and the neutral form in
charge. I was confused about how to interpret the results. Can I use
the results with the same sign or should I change sings?

  kind regard,

servaas
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