[gmx-users] Duplicated dihedral lines on .prm file

[Daniel Burns]

Hello,

I am trying to simulate a dimer with identical ligands bound on each
subunit.

I generated the ligand files with cgenff.

I have Liga and Ligb files that each have identical contents (the
filenames, residue, and molecule name are different though).  I am only
getting errors on the Ligb.prm file in the [dihedral types] section.  The
problematic section repeats the i, j, k, and l atoms for 3 or more lines
but each line has different phi and kphi values.  The error is shown below
along with the section of the ligb.prm file that presents the issue.


Thank you for your time!

Dan

ERROR 9 [file ligb.prm, line 42]:

  Encountered a second block of parameters for dihedral type 9 for the same

  atoms, with either different parameters and/or the first block has

  multiple lines. This is not supported.


The troublesome lines from ligb.prm:


CG2R61   CG2R61    CG321   NG2R51     9     0.000000     0.497896     2
  CG2R61   CG2R61    CG321   NG2R51     9   180.000000     0.552288     4
  CG2R61   CG2R61    CG321   NG2R51     9   180.000000     0.054392     6
  CG2R61    CG321   NG2R51   CG2R51     9     0.000000     1.610840     1
  CG2R61    CG321   NG2R51   CG2R51     9     0.000000     1.757280     2
  CG2R61    CG321   NG2R51   CG2R51     9     0.000000     0.334720     3
  CG2R61    CG321   NG2R51   CG2R51     9     0.000000     0.230120     4
  CG2R61    CG321   NG2R51   NG2R50     9   180.000000     1.610840     1
  CG2R61    CG321   NG2R51   NG2R50     9     0.000000     1.757280     2
  CG2R61    CG321   NG2R51   NG2R50     9   180.000000     0.334720     3
  CG2R61    CG321   NG2R51   NG2R50     9     0.000000     0.230120     4