Dear Gromacs Users. I generated a topology file of GDP for OPLSAA force field using MKTOP. But on running grompp I got a list of No default Angle types and No default Ryckaert Bell. types error. So this time i manually assigned the appropriate atom types by looking up the atomtypes.atp file and managed to come down from 24 errors to 9 errors. All the errors correspond to missing dihedrals only. I notice that these missing dihedrals are concentrated around two specific region of the structures which are the Pyramidine ring of Guanine and the bond connecting the C1 atom of ribose and N9 atom of the imidazole ring of Guanine.
So i have a two part query: 1. I had assigned the atom types for the Guanine part of GDP from the already defined atom types for Guanine in the library. Is it not then surprising to get 6 missing dihedrals for the pyramidine ring considering the fact that Guanine is already parameterized ? Am i wrong in this ? 2. In an effort to remove the missing dihedral errors related to the C1-N9 region it tried to manually add the missing diherals to the ffbonded.itp file. I noticed one of the missing dihedral was: OH-CT-CT-NA (O2'-C2'-C1'-N9). So i added the dihedral entry as: NA CT CT OH 3 16.73600 -16.73600 0.00000 0.00000 0.00000 0.00000 based on an already defined dihedral: NT CT CT OH 3 16.73600 -16.73600 0.00000 0.00000 0.00000 0.00000. But the error corresponding to this dihedral remained on re-run. Is there anything wrong with this ? Do i need to edit some other related files. I am very new to gromacs. Kindly help as I'm stuck. Thanks in advance. Abhishek Acharya M.Tech Structural Biology Lab Biological Sciences and Bioengineering Department Indian Institute of Technology Kanpur. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists