Hello all,
While double checking to make sure I had set my system up properly, I was
looking through the charges and realized that the charge on protonated
histidine inside of Amberff03 did not add up to +1 (they add up to about
+0.45). I cross referenced the DESMOND implementation of the Amber03 force
field and noticed that they had flipped a few signs around. In particular,
the CA, HA, and ND1 have their signs flipped in DESMOND. The charges in
the DESMOND implementation correctly sum up to 1.
I saw this mentioned earlier in the mailing list (
http://archive.ambermd.org/200803/0171.html) and I noticed that Dr.
Walker's charges match those in the DESMOND implementation, whereas the
original poster's charges match those in my own Amber force field file;
this discrepancy is not addressed in that former email. I am using
Amber12/AmberTools13. The tools were just updated yesterday. Any thoughts?
Thanks!
---
Adam Pratt
Graduate Student in Chemistry
Chong Lab, Room 338, Eberly Hall
University of Pittsburgh
Pittsburgh, PA 15260
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 24 2013 - 12:30:02 PDT
