[AMBER] AMBER18/16 12-6-4LJ Sander TI problem

From: Paulius Kantakevicius <paulius.kantakevicius.gmail.com>
Date: Tue, 12 Nov 2019 12:58:51 +0200


I experienced problems to reproduce the HFE values of 2+ and 3+ ions cited
in papers (https://pubs.acs.org/doi/10.1021/ct400751u
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306492/) using 12-6-4LJ
potentials on AMBER18 and AMBER16. I am using Sander engine and I added the
C4 terms using Parmed from AmberTools19, however the desolvation energy
values I obtained are off: Ca2+ I obtained desolvation energy of 348.9
kcal/mol (350.1 from charge removal and -2.2 from VdW removal) -
experimental is 359.7 kcal/mol, whereas for Mg2+ I got 410.7 kcal/mol
(412.8 from charge removal and -2.1 from VdW removal) - experimental is
437.4 kcal/mol. I tried running Y3+ ion as well, for which I obtained 788.2
kcal/mol whereas experimental value is 824.6 kcal/mol.

I tried running Ca2+ ion without adding C4 term and I got HFE values
further from experimental ~337 kcal/mol indicating that Sander uses C4 term
in TI calculations.
Then I tried running Ca2+ and Mg2+ ions using different set of parameters
from older paper (https://pubs.acs.org/doi/10.1021/ct400146w) that were
made for 12-6LJ (frcmod.ions234lm_hfe_tip3p) and have to reproduce HFE
values accurately but coordination numbers and IODs with errors to see
whether they will produce accurate HFE values. And they indeed produced
values, which were very close to experimental values: 360.4 kcal/mol for
Ca2+ and 437.5 kcal/mol. Therefore, I suspect that there is an issue in
AMBER16 and AMBER18 in implementation of C4 term in TI calculations for
Sander engine.

Also, I noticed that some 12-6LJ parameter files in AmberTools19 contain
wrong parameters:
in frcmod.ions234lm_hfe_tip3p file for 3+ and 4+ ions instead of HFE values
from the https://pubs.acs.org/doi/10.1021/jp505875v paper IOD values are
entered instead and in frcmod.ions234lm_iod_tip3p file for 3+ and 4+ ions
instead of IOD values 12-6-4LJ values are shown instead.

I would greatly appreciate if someone would inspect the TI calculations for
12-6-4LJ on the Sander engine on either AMBER16 or AMBER18 version or could
help solve this issue in any other way.

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Received on Tue Nov 12 2019 - 03:00:02 PST
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