Re: [AMBER] Issues with 12-6-4

From: Li, Zhen via AMBER <amber.ambermd.org>
Date: Fri, 14 Feb 2025 19:35:56 +0000

Hi Nell,

Could you kindly reveal two things? (1) “%FLAG AMBER_ATOM_TYPE %FORMAT(20a4)” section of your PRMTOP file and (2) the ParmEd output?

I suspect that either the “HG2” atom type is not recognized or that ParmEd is not picking the atom as intended.

Thank you!

Best regards,
Zhen.

From: Nell Karpinski via AMBER <amber.ambermd.org>
Date: Friday, February 14, 2025 at 2:30 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Issues with 12-6-4
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
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Received on Fri Feb 14 2025 - 12:00:02 PST