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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Received on Sun May 27 2007 - 06:07:26 PDT
