I am using Gromacs 4.5.5. In my residuetypes.dat ACE is correctly listed as protein residue and pdb2gmx doesn't give any error about protein type.
For clarity I copy here my pdb, the interesting parts of the aminoacids.rtp file and the pdb2gmx command. Thank you very much for any help you can give. ##################################### FROM aminoacids.rtp ##################################### [ ACE ] [ atoms ] CA CH3 0.000 0 C C 0.380 1 O O -0.380 1 [ bonds ] C CA gb_26 C O gb_4 C +N gb_9 [ angles ] CA C O ga_30 CA C +N ga_18 O C +N ga_32 [ impropers ] C CA +N O gi_1 [ ALA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH3 0.00000 1 C C 0.380 2 O O -0.380 2 [ 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 [ 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 [ 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 [ NAC ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH3 0.00000 0 [ bonds ] N CA gb_20 N H gb_2 -C N gb_9 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 ##################################### pdb file ##################################### TER ##################################### pdb2gmx ##################################### pdb2gmx -f Ac_A_NHMe/Ac_A_NHMe_gromos.pdb -o Ac_A_NHMe/Ac_A_NHMe.gro -p Ac_A_NHMe/Ac_A_NHMe.top -i Ac_A_NHMe/Ac_A_NHMe.itp -n Ac_A_NHMe/Ac_A_NHMe.ndx -q Ac_A_NHMe/Ac_A_NHMe.pdb -ignh -ter :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description ------------------------------------------------------------ -f Ac_A_NHMe/Ac_A_NHMe_gromos.pdb Input Structure file: gro g96 pdb Reading Ac_A_NHMe/Ac_A_NHMe_gromos.pdb... Read 'ACETYL-ALANINE-METHYLAMIDE', 10 atoms Back Off! I just backed up Ac_A_NHMe/Ac_A_NHMe.pdb to Ac_A_NHMe/#Ac_A_NHMe.pdb.5# Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 0 residues with 10 atoms chain #res #atoms 1 'A' 1 1 2 ' ' 3 9 All occupancies are one Opening force field file ./gromos43a1_modifiedwithNAC.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos43a1_modifiedwithNAC) Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.rtp Residue 97 Sorting it all out... Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.hdb Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.n.tdb Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.c.tdb Back Off! I just backed up Ac_A_NHMe/Ac_A_NHMe.top to Ac_A_NHMe/#Ac_A_NHMe.top.5# Processing chain 1 'A' (1 atoms, 1 residues) Identified residue ACE1 as a starting terminus. Identified residue ACE1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: None 2 Start terminus ACE-1: None Select end terminus type for ACE-1 0: COO- 1: COOH 2: None 2 End terminus ACE-1: None ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1034 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Francesca -- View this message in context: http://gromacs.5086.x6.nabble.com/C-terminus-residue-name-in-Gromos43a1-tp5014776p5014844.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.