Hello Akhil,
You should use a nstlim value that gives you a converged fraction of protonation in the production run. The choice is system dependent, but I would say you need to run at least 10 ns minimum.
What finddgref.py does at the very beginning is to run very short simulations to get a quick sense of where the delta G reference should be. With nstlim=50 and ntcnstph=5, your cpout file must have 5 entries. So, it should not be blank. Did you check your mdout file to ensure the simulation ran successfully?
I hope this helps,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
On Jan 31, 2023, at 8:24 AM, Akhil Sudarsan via AMBER <amber.ambermd.org> wrote:
Dear AMBER users,
I am trying to find the relative energies of the protonation states of my model system using the finddgref.py tool to add it to the list of titratable residues. The system I am using is an ionizable lipid. However when I try to execute the finddgref.py script, I can see that the value of the number of steps (nstlim) gets reduced from 10,00,000 in the md.mdin file to 50 in the md.mdin.temporary file. This results in a blank cpout file and I do not get any information of the relative energies. The template for the md.mdin input file was taken from the constant pH simulation tutorial in the AMBER website (
https://ambermd.org/tutorials/advanced/tutorial18/section3.htm). How can I fix this?
Log file:
Checking cpin file and/or cein file.
We are going to find DELTAGREF for a pH titratable residue without using Replica Exchange.
The solvent pH value is 9.470 and was loaded from the mdin file (md.mdin).
The temperature is 300.00 K and was loaded from the mdin file (md.mdin).
According to the mdin file (md.mdin), the value of ntcnstph is 5.
According to the mdin file (md.mdin), the value of nstlim is 1000000.
The program will try to find a range of values for DELTAGREF automatically, as the argument -dgrefrange was not given
AMBER execution #1: running 50 MD steps for DELTAGREF = 0.000000 kcal/mol
ERROR: Could not read the fraction of protonated or reduced species from the output of cphstats or cestats. The command executed was:
cphstats -i mc3h-head1.cpin.temporary mc3h.cpout
The execution of finddgref.py stopped
Best Regards,
Akhil Sudarsan
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Received on Tue Jan 31 2023 - 09:30:02 PST
