Dear Justin I was really confused. I know that my peroblem is in incorrect entries (LYS2 and GLU2) in aminoacids.rtp file
Sinse I want to have a isopeptide bond between (CD atom of GLU residue from chain B and NZ atom of LYS residue from chain E), thus I should use one HZ atom (for LYS2) and one OE atom (for GLU2) as follows. Is my vision true? [ GLU2 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD C 0.50000 2 OE OM -0.50000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE gb_5 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE ga_21 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 [ LYS2 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 3 NZ NT -0.50000 3 HZ H 0.50000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_10 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ HZ gd_14 ---------------------------------------------------------------------------- Unfortunately, after using pdb2gmx, I encountered with: Linking CYS-252 SG-248 and CYS-312 SG-743... Linking CYS-358 SG-1094 and CYS-416 SG-1565... Linking GLU-380 CD-1269 and LYS-540 NZ-2499... Start terminus PRO-220: PRO-NH2+ End terminus HIS-434: COO- Start terminus GLY-435: GLY-NH3+ End terminus LYS-551: COO- ------------------------------------------------------- Program gmx, VERSION 5.0.5 Source code file: /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732 Fatal error: Atom OE1 in residue GLU 380 was not found in rtp entry GLU2 with 9 atoms while sorting atoms. ------------------------------------------------------- I made GLU2 and LYS2 based on isopeptide bond, what is the resaon of this error? Thanks in advance. -- 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.