Dear Amber-ers,
I am trying to calculate the solvation energy of Na+ in water with
thermodynamics integration implemented in amber11, sander.
I had appled the patch "bugfix.all" when I compile sander in March this
year.
I copied parameters from ponder's webpage to
amber11/dat/leap/parm/amoebapro.prm, created a Na+ offlib file by taking
data from
amber11/dat/leap/lib/ions08.lib and change the atom type from "Na+" to 205,
as the original amoeba forefield in amber11 does not
have Na+'s parameters.
when I calculated the energy cost to turn on the charge of amoeba Na+, I
found the DV/DL is alyways 0. I also try calculating the enery
cost of Na+ with amber99 force field and the same input files (starting
prmtop and crd files are created from amber99 forcefield), and it
seems OK, yielding no-zero dv/dl's.
I also calculated the energy cost to turn on the LJ, but the amoeba ff seems
to assign ntf as 8, which conflicts with soft core potential
(please see the end of Na_test/LJ_amoeba/equi_v1_l1.out). when I turn off
soft core, the simulation just died. I also try this calculation
with amber99 ff with the same input files, and it works.
I am wondering if amoeba ff is imcompatible with free energy calculation, or
if there is some trick or patch I need to use (e.g. I remember
there is a tutorial which calculate LJ part solvation free energy without
soft core. it is different from what I did, sure. Or I can try BAR method)?
The force field, offlib that I used, the parameters that I added into the
original ff. The script that I used to create the starting prmtop crd files,
and the outputs are in the attached tar files.
Your kind help will be greatly appreciated.
Thank you.
yours
libo, NY
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Received on Fri Aug 05 2011 - 13:30:02 PDT
