Hello,
I am following the "Modeling a Magnesium-DNA System using the 12-6-4
LJ-Type Nonbonded Model, Example A" tutorial to use LJ_1264 for Hg2+. I am
attempting to use 'add_12_6_4 :HG2', however, I am getting all zeros for
my LJ CCoeff.
%FLAG LENNARD_JONES_CCOEF
%COMMENT For 12-6-4 potential used for divalent metal ions
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
I have tried to use parmed with Amber/18.0, Amber/22.0, and Amber/24.0, but
I obtain the same result.
My parmed.in file contents are:
loadRestrt hg_final_mango_ligand.inpcrd
setOverwrite True
add12_6_4 :HG2 watermodel SPCE
outparm hg_final_mango_ligand_1264.prmtop hg_final_mango_ligand_1264.inpcrd
Am I doing something wrong here? Please let me know, thank you in advance!
All the best,
Nell
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 14 2025 - 11:30:02 PST
