From: Amy Rice (
Date: Thu Sep 17 2015 - 14:39:05 CDT

Hi all,
I am attempting to parameterize a modified arginine residue following the
ffTK screencasts, using VMD 1.9.2. I've been able to complete the first 4
steps without issue, but I'm running into some errors during the charge
optimization, in both downhill mode and simulated annealing. The error
message reads:
"can't read "ljPars(HA2 HA2 HA2 H)": no such element in array"

I noticed a similar problem was discussed previously (, however
as far as I can tell the atom types HA2 and H exist in both the psf and
parm files. I have LJ parameters in my .par file for both of these atom
types, so I'm not sure why I'm receiving an error. I've attached my
preliminary psf, pdb, and par for reference. Note that I am also loading
the charmm 36 protein prm as an input paramter file.

Thank you for the help,
- Amy

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology