Re: energy difference between HSE and HSD

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue May 09 2017 - 11:28:52 CDT

On 9 May 2017 at 18:12, Radak, Brian K <bradak_at_anl.gov> wrote:

> I based that on the free energy of transformation between the HSE and HSD
> topologies in solution
>

That number is not supposed to mean anything in particular, because the HSE
and HSD topologies lack a common energy reference.

, which is ~16 kcal/mol when NMR gives a result more like ~-1 kcal/mol
> (note that the sign is also different).
>
> You raise a good point. Should the force field model even produce such a
> result? The covalent bond energies are probably extremely important here
> and the force field has no physical description of those effects. One could
> try looking up tabulated bond energies and making an adjustment, but that
> seems rather ad hoc.
>

Indeed, I don't see how you can describe tautomerism without some form of
electronic structure calculation on those species.

Jerome

> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
> ------------------------------
> *From:* Jérôme Hénin [jerome.henin_at_ibpc.fr]
> *Sent:* Tuesday, May 09, 2017 10:51 AM
> *To:* Namd Mailing List; Radak, Brian K
> *Cc:* Hao Dong
> *Subject:* Re: namd-l: energy difference between HSE and HSD
>
> I must missing something here. How is a FF of this type supposed to
> reproduce a tautomerization energy? How do you calculate a tautomer ratio
> from C36?
>
> Jerome
>
> On 9 May 2017 at 17:43, Radak, Brian K <bradak_at_anl.gov> wrote:
>
>> The HSE and HSD parameters were clearly not designed to reproduce
>> tautomerization energies. The C36 force field does in fact get the tautomer
>> ratio wrong in solution (by a LOT).
>>
>> Maybe this will be improved in future force field versions?
>>
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
>> brian.radak_at_anl.gov
>> ------------------------------
>> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
>> Hao Dong [donghaonj_at_gmail.com]
>> *Sent:* Monday, May 08, 2017 11:48 PM
>> *To:* namd-l_at_ks.uiuc.edu
>> *Subject:* namd-l: energy difference between HSE and HSD
>>
>> Dear all,
>>
>> I built two pdb files to calculate the energy difference between
>> residues HSE and HSD, that is Histidine in different protonated states
>> (the structures are "ACE-HSD-CT2" and “ACE-HSE-CT2”).
>>
>> I tried Charmm36 force field and got E(HSD)-E(HSE)=13kcal/mol. Then I
>> used Gaussian(b3lyp/6-311g(d,p)) and Amber force field to calculate the
>> energy, it came out that: E(HSD)-E(HSE)=1-2kcal/mol.
>>
>> Obviously, 13kcal/mol is too large for this situation. I checked the NAMD
>> output files and found great gap in ELECT energy, which made me very
>> confused. Why the energy difference between the two forms were
>> overestimated by using Charmm36 force field ?
>>
>> Here is my input file:
>> minimization on
>> numsteps 0
>>
>> set targetemp 310.0
>> set coorfile hsd_1.pdb
>> coordinates $coorfile
>> structure hsd_1.psf
>>
>> outputname myout1
>> restartname myrst1
>> outputEnergies 1
>> binaryoutput no
>> xstFreq 1
>> DCDFreq 1
>> restartFreq 1
>>
>> COMmotion no
>> timestep 1.0 ;# 2fs/step
>> nonbondedFreq 1
>> fullElectFrequency 2
>> temperature $targetemp
>>
>> paraTypeCharmm on
>> parameters par_all36_prot_wat_ions.prm
>>
>> exclude scaled1-4
>> 1-4scaling 1.0
>> dielectric 1.0
>> switching on
>> switchdist 10.0
>> cutoff 12.0
>> pairlistdist 14.0 ;# cutoff + 2
>> stepspercycle 10
>>
>
>

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