Thank you! Should my ligands have identical names in the .gro file?
On Fri, Nov 8, 2019 at 6:23 PM Justin Lemkul <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
