Hi all, As per a previous email (cross linking two peptide chains), I¹ve created a brand new crosslink (think disulphide bond) residue from scratch. I have defined it in all the files necessary (.rtp, residuetypes, specbond, atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no problems.
Unfortunately when I run grompp (5.0.4) I get the following error: Fatal error: Unknown bond_atomtype MN1 <‹‹ first atom in my new residue At first I thought my topology might be pointing to the wrong forcefield, but I¹ve checked and double checked: #include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp" #include "modic.itp" ;#ifdef POSRES ;#include "posre.itp" ;#endif [ system ] ; Name MODIC with glycine terminal ends [ molecules ] ; Compound #mols MODIC 1 I¹m going to take a guess at what the problem is. Each of the atoms in the residue was derived from scratch.Therefore, they have a completely new type. I wasn¹t feeling very creative with my naming convention so the atom name and the atom type are identical e.g., ;MODIC crosslink [ MOD1 ] [ atoms ] ; NAME TYPE CHARGE NUMBER MN1 MN1 -0.3640 1 MC1 MC1 0.0358 2 MC15 MC15 0.4871 3 Š Š Will this have confused grompp? Many thanks Anthony Dr Anthony Nash Department of Chemistry University College London -- 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.
