From: Hugh Martin (hughtendo_at_gmail.com)
Date: Mon Jul 06 2009 - 10:39:38 CDT
Hello,
I am attempting to use ABF to induce the translocation of a 20-base
polynucleotide through a protein pore and am having some trouble getting the
system to work in the way that I was expecting. I have tested the tutorial
files with success but have not been able to apply the technique to my
system.
I realise that it is difficult for others to comment on using ABF in an
unfamiliar system, so listed below is what I believe to be the key
information for consideration:
The alpha carbons of the protein pore are constrained to maintain their
positions.
One set of alpha carbons belonging to a protein pore residue is used as
"abf1" for the reference point to "abf2"s translocation. Given that abf1's
position is constrained (see above point), I presume that is will allow
consistent translocation of abf2.
The atom I wish to translocate is the leading atom of the polynucleotide
(thus pulling the whole molecule with it).
The precise z-axis separation of abf1 and abf2 begins as -34.4900016784
Angstroms.
I wish to translocate the polynucleotide molecule from -34.5 to -42.5
separation.
The problem is that no matter what alterations I seem to make to the input
parameters, the abf2 atom simply moves very quickly from xiMin to the middle
of xiMin and xiMax, and remains within roughly +/- 0.3 Angstroms of the
precise middle of those two values for the remainder of the simulation. If I
have understood ABF correctly, I believe that the ABF scripts should sample
the system while the abf2 atom resides within each dxi bin starting from
xiMin and ending with xiMax, and once each dxi bin has been sampled "abf
fullSamples" number of times, the adaptive biasing force will allow abf2 to
overcome energy barriers in order to move to the next dxi bin, though the
movement is also dependent on the abf2 atom's self diffusion properties.
The fact that it so quickly moves to the middle of xiMin and xiMax shows
that I have either set up the simulation incorrectly, that I have
misunderstood what is supposed to occur during the simulation, or that my
system is not compatible with the ABF technique. Any clues as to which of
these three may be the case would be greatly appreciated.
Listed below is an example of my ABF input parameters in the conf file,
though I have also run test simulations with altered parameters, in
particular "abf xiMin", "abf xiMax", "abf dxi", "abf fullSamples", and
"numsteps" in order to try and resolve the issue:
# ABF SECTION
source ../abf-1.8/abf.tcl
# ORDER PARAMETER
abf coordinate zCoord-1atom
# abf1 atoms are the CA atoms of protein resid 8, abf2 is the pulling atom
abf abf1 {122863 95173 99788 104403 109018 113633 118248}
abf abf2 262093
# precise xiMin is -34.4900016784
abf xiMin -34.5
abf xiMax -42.5
abf dxi 0.4
# SAMPLING
abf fullSamples 100
abf dSmooth 0.1
abf forceConst 10.0
# OUTPUT
abf writeXiFreq 200
abf outFile abf_window1.abf
# MD SETUP
numsteps 600000
Many thanks,
Hugh
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