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

[Justin Lemkul]

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

==================================================