dear list, I want to restrain a group of atoms within one sphere. I got the sphere center coordinate using g_traj
In topol.top I added this part: #ifdef POSRES_FLATBOTTOM [ position_restraints ] ; i funct g r(nm) k (kJ/mol/nm) 4 2 1 1.5 300000 857 2 1 1.5 300000 1715 2 1 1.5 300000 #endif and in the reference file I put: ATOM 4 CA GLY 704 21.698 27.798 9.333 1.00 0.00 C ATOM 857 CA GLY 704 21.698 27.798 9.333 1.00 0.00 C ATOM 1715 CA GLY 704 21.698 27.798 9.333 1.00 0.00 C but I came across this error: WARNING 1 [file topol.top, line 16661]: The number of atoms in flat.pdb (3) does not match the number of atoms in the topology (97123). Will assume that the first 3 atoms in the topology and flat.pdb match. could anybody tell me what's wrong with my -r file? it goes well without giving reference file. thanks in advance. Jinmei -- 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 [email protected].
