Hi Paulius,
I have received the email and will get back to you later. I have attached in this email the corrected version for the following four files:
(1) frcmod.ions234lm_hfe_tip3p
(2) frcmod.ions234lm_iod_tip3p
(3) frcmod.ions234lm_126_tip3p
(4) frcmod.ions234lm_hfe_tip4pew
Please use them to replace the old files. This also applies to other users who are using AMBER 2016-2019.
Thanks again for finding the errors!
Yours sincerely,
Pengfei
> On Nov 16, 2019, at 6:20 AM, Paulius Kantakevicius <paulius.kantakevicius.gmail.com> wrote:
>
> Hi Pengfei,
>
> Thank you for your response! I sent out .inpcrd and .prmtop files as you
> asked to ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>.
>
> Regards,
> Paulius
>
> On Sat, Nov 16, 2019 at 1:32 AM Pengfei Li <ambermailpengfei.gmail.com <mailto: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> <mailto: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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>>
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Received on Sat Nov 16 2019 - 18:30:02 PST
