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

[Daniel Burns]

Thank you!

Should my ligands have identical names in the .gro file?

On Fri, Nov 8, 2019 at 6:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/8/19 4:25 PM, Daniel Burns wrote:
> > 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
>
> If the ligands are topologically identical, their bonded parameters can
> only appear once in the topology. You can't simply #include both
> topologies (despite giving them different [moleculetype] names) because
> their bonded parameters will be repeated, therefore triggering this error.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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