Hello Tu,
+ or - inf values indicate that your range of pH values is significantly off from your pKa. You should simulate more pH values in order to make pKa predictions for residues where this is happening.
I hope this helps.
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
________________________________
From: Hoang, Oanh Tu via AMBER <amber.ambermd.org>
Sent: Wednesday, May 24, 2023 2:42 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] inf pKa values constant pH
Hello,
I am doing constant pH MD with AMBER and in the pKa output I get some inf and -inf values. If i want to calculate the average of the pKa or plot the results, should I leave the inf values out or do I have to set inf = 14 and -inf=-14 or 0?
Or would it be the best to take the average of the population and calculate the pKa with the Hendersen-Hasselbach equation?
Thank you in advance!
Best,
Tu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 24 2023 - 21:00:03 PDT
