Dear All, In the on-line protein-ligand md tutorial, related to the drg.itp file, there is
"Let's take a look at the [ atoms ] section of our JZ4 topology: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 JZ4 C4 1 0.000 15.0350 2 CH2 1 JZ4 C14 2 0.059 14.0270 3 CH2 1 JZ4 C13 2 0.060 14.0270 4 C 1 JZ4 C12 2 -0.041 12.0110 5 CR1 1 JZ4 C11 2 -0.026 12.0110 6 HC 1 JZ4 H11 2 0.006 1.0080 7 CR1 1 JZ4 C7 2 -0.026 12.0110 8 HC 1 JZ4 H7 2 0.006 1.0080 9 CR1 1 JZ4 C8 2 -0.026 12.0110 10 HC 1 JZ4 H8 2 0.007 1.0080 11 CR1 1 JZ4 C9 2 -0.026 12.0110 12 HC 1 JZ4 H9 2 0.007 1.0080 13 C 1 JZ4 C10 3 0.137 12.0110 14 OA 1 JZ4 OAB 3 -0.172 15.9994 15 H 1 JZ4 HAB 3 0.035 1.0080". May I ask, for the drg.itp file, we only need contain the [ atoms ] section, all we should contain every sections of the original drg.itp file? Secondly, suppose my ligand itp was not got by the traditional gromacs forcefiled, in this situation should we modify the atom types database we got when we originally installed the gromacs to include the atom types specified for the ligand, or we can have the ligand.itp contains a section with the specific ligand atom types information supplied? Brett -- 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.