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.
