From: Hao Dong (donghaonj_at_gmail.com)
Date: Mon May 08 2017 - 23:48:48 CDT
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:
set targetemp 310.0
set coorfile hsd_1.pdb
timestep 1.0 ;# 2fs/step
pairlistdist 14.0 ;# cutoff + 2
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