Hi Pengfei,
Thank you for your response! I sent out .inpcrd and .prmtop files as you
asked to ambermailpengfei.gmail.com.
Regards,
Paulius
On Sat, Nov 16, 2019 at 1:32 AM Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Paulius,
>
> Thanks for your email.
>
> > On Nov 12, 2019, at 5:58 AM, Paulius Kantakevicius <
> paulius.kantakevicius.gmail.com> wrote:
> >
> > Hello,
> >
> > 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.
> >
>
> Can you send these input prmtop and inpcrd files (after adding C4 terms)
> to my email: ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>?
> I can help to do a check.
>
> > 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 checked the parameter files, you are right.
>
> I apologize for these stupid mistakes, and thank you very much for finding
> them! I checked the git log and found these mistakes were made when I
> merged the parameter files in 2016: the parameters in AMBER 2015 were
> correct for the +3 and +4 ions, but afterwards the following parameter
> files were messed up because of my stupid mistakes:
>
> (1) the file frcmod.ions234lm_hfe_tip3p should have HFE parameter set, but
> has IOD parameter set for the +3 and +4 ions in the TIP3P water model
> (2) the file frcmod.ions234lm_iod_tip3p should have IOD parameter set, but
> has 12-6-4 parameter set for the +3 and +4 ions in the TIP3P water model,
> note that only the Rmin/2 and epsilon parameters in the file, while the C4
> terms are still need to be added by the ParmEd program.
> (3) the file frcmod.ions234lm_126_tip3p should have IOD parameter set, but
> has 12-6-4 parameter set for the +3 and +4 ions in the TIP3P water model,
> note that only the Rmin/2 and epsilon parameters in the file, while the C4
> terms are still need to be added by the ParmEd program.
> (4) the file frcmod.ions234lm_hfe_tip4pew should have HFE parameter set,
> but has IOD parameter for the +3 and +4 ions in TIP4PEW water model
>
> It seems the other parameter files about +3 and +4 ions are fine. The
> fortunate part out of all the misfortunes is that the VDW parameters in the
> IOD and 12-6-4 parameter sets are not too far away from each other (Rmin/2
> usually within 0.1 Angstrom with each other), and the HFE parameters for +3
> and +4 are usually not used in MD simulations because their big errors for
> simulating the structural properties like IOD.
>
> I am very sorry for any inconveniences these mistakes brought to the
> community… I will create a git commit to correct these mistakes later this
> week.
>
> Yours sincerely,
> Pengfei
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Received on Sat Nov 16 2019 - 03:30:02 PST
