Hello. I want to calculate the pka of two residues and I have decided to
use the constant pH simulations in amber to calculate the titration curves
of these residues. I am running replica exchange with constant pH and I am
trying to follow the "tutorial" given in
http://jswails.wikidot.com/ph-replica-exchange#toc4
I 've noticed a few disparities between what is shown on that wiki and what
really happens with my calculations. A few discrepancies include:
The ntxo flag is set to 2 in the mdin file for the replica exchange
calculations, but I found no such value on the manual.
The page says "When running replica exchange simulations, the format of the
cpout file is slightly changed so that the current target pH value is
printed next to each record". But this is not what has happened here. My
cpout files contain:
Solvent pH: 3.50000
Monte Carlo step size: 5
Time step: 5
Time: 1000.008
Residue 0 State: 0
Residue 1 State: 0
Residue 1 State: 0
Residue 1 State: 0
.
..
But no pH value is printed next to each record.
I have put a hold on the simulations in order to check if pH-REMD
simulations are still a working feature in amber12 and if this is the
behaviour I should expect from the simulations.
Below is a copy of one of my mdin file and of the groupfile used.
mdin >
&cntrl
icnstph=1, dt=0.002, ioutfm=1,
nstlim=100, ig=-1, ntb=0, numexchg=5000,
ntwr=1000, ntwx=1000, irest=1,
cut=1000.0, ntcnstph=5, ntpr=1000,
ntx=5, solvph=2.5, saltcon=0.1, ntt=3,
ntc=2, ntf=2, gamma_ln=10.0, igb=2, temp0=298,
/
groupfile >
-O -i pH0/pH_0.mdin -p HOH_igb.prmtop -c restrt.heat -cpin HOH_igb.cpin -o
pH0/ph0.md1.mdout -cpout pH0/pH0.md1.cpout -cprestrt pH0/pH0.md1.cpin -r
pH0/pH0.md1.rstrt -inf pH0/pH0.md1.mdinfo -rem 3 -remlog rem.md1.log
-remtype rem_md1.type -x pH0/pH0.md1.mdcrd
..
..continues for the other 7 pH values......
Thank you
Fabrício
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Received on Thu Aug 29 2013 - 14:30:02 PDT
