From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue May 09 2017 - 10:51:00 CDT
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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