energy difference between HSE and HSD

From: Hao Dong (
Date: Mon May 08 2017 - 23:48:48 CDT

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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