Respected Sir/Ma'am,
I have performed a Constant pH simulation at pH 4.8 following the AMBER
tutorial and there is only one titratable residue in my peptide.
I have used ntwx=2500.
My goal is to extract the protonation state of the titratable residue for
all saved conformations during my production runs (saved at every 2500
steps).
For this, I tried to extract the information from "cpout" files because in
the manual it is written that "Full records are written on the first step
and every ntwx steps afterwards so as to coincide with the frames written
to the trajectory".
But when I looked into the cpout file I found there is a discrepancy in the
Time stamp. Bellow I have highlighted an example.
Solvent pH: 4.80000
Monte Carlo step size: 50
Time step: 25000000
Time: *50999.998*
Residue 0 State: 0
So my questions are:
1. Is this the way Amber writes protonation state information for the frame
saved at 51000ps?
2. Could I use the protonation state information saved for Time: 50999.998
in the cpout file for the frame saved for 51000ps?
Thank you,
Saikat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 05 2018 - 06:00:03 PDT
