Hello everyone<br><br>I am trying to set up a nucleic acid only simulation using gromacs 4.5.2<br><br>pdb2gmx is giving me only options to cap protein terminals and when I choose none it gives the error:<br><br>"There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry."<br>
<br>and exits.<br><br>below is the program output.<br><br>Alpay<br><br><br>452pdb2gmx -f chr13_115016196_gaa_3loop_h.pdb -o conf.pdb -p -inter<br> :-) G R O M A C S (-:<br><br> Good gRace! Old Maple Actually Chews Slate<br>
<br> :-) VERSION 4.5-beta2 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) 452pdb2gmx (double precision) (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f chr13_115016196_gaa_3loop_h.pdb Input Structure file: gro g96<br>
pdb tpr etc.<br> -o conf.pdb Output Structure file: gro g96 pdb etc.<br> -p topol.top Output Topology file<br> -i posre.itp Output Include file for topology<br>
-n clean.ndx Output, Opt. Index file<br> -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.<br><br>Option Type Value Description<br>------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>-[no]version bool no Print version info and quit<br>-nice int 0 Set the nicelevel<br>-[no]cwd bool no Also read force field files from the current<br>
working directory<br>-[no]rtpo bool no Allow an entry in a local rtp file to override a<br> library rtp entry<br>-chainsep enum id_or_ter Condition in PDB files when a new chain should<br>
be started: id_or_ter, id_and_ter, ter, id or<br> interactive<br>-ff string select Force field, interactive by default. Use -h for<br> information.<br>
-water enum select Water model to use: select, none, spc, spce,<br> tip3p, tip4p or tip5p<br>-[no]inter bool yes Set the next 8 options to interactive<br>-[no]ss bool no Interactive SS bridge selection<br>
-[no]ter bool no Interactive termini selection, iso charged<br>-[no]lys bool no Interactive Lysine selection, iso charged<br>-[no]arg bool no Interactive Arganine selection, iso charged<br>
-[no]asp bool no Interactive Aspartic Acid selection, iso charged<br>-[no]glu bool no Interactive Glutamic Acid selection, iso charged<br>-[no]gln bool no Interactive Glutamine selection, iso neutral<br>
-[no]his bool no Interactive Histidine selection, iso checking<br> H-bonds<br>-angle real 135 Minimum hydrogen-donor-acceptor angle for a<br> H-bond (degrees)<br>
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)<br>-[no]una bool no Select aromatic rings with united CH atoms on<br> Phenylalanine, Tryptophane and Tyrosine<br>
-[no]ignh bool no Ignore hydrogen atoms that are in the pdb file<br>-[no]missing bool no Continue when atoms are missing, dangerous<br>-[no]v bool no Be slightly more verbose in messages<br>-posrefc real 1000 Force constant for position restraints<br>
-vsite enum none Convert atoms to virtual sites: none, hydrogens<br> or aromatics<br>-[no]heavyh bool no Make hydrogen atoms heavy<br>-[no]deuterate bool no Change the mass of hydrogens to 2 amu<br>
-[no]chargegrp bool yes Use charge groups in the rtp file<br>-[no]cmap bool yes Use cmap torsions (if enabled in the rtp file)<br>-[no]renum bool no Renumber the residues consecutively in the output<br>
-[no]rtpres bool no Use rtp entry names as residue names<br><br><br>Select the Force Field:<br> 1: AMBER03_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br> 2: AMBER94_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br> 3: AMBER96_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br>
4: AMBER99_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br> 5: AMBER99SB-ILDN_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br> 6: AMBER99SB_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br> 7: AMBERGS_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION<br> 8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta<br>
9: GROMOS96 43a1 force field<br>10: GROMOS96 43a2 force field (improved alkane dihedrals)<br>11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>15: [DEPRECATED] Encad all-atom force field, using full solvent charges<br>16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges<br>
17: [DEPRECATED] Gromacs force field (see manual)<br>18: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>13<br><br>Using the Gromos53a6 force field in directory /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff<br>
<br>Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/watermodels.dat<br><br>Select the Water Model:<br> 1: SPC simple point charge, recommended<br> 2: SPC/E extended simple point charge<br>
3: None<br>1<br>Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.r2b<br>Reading chr13_115016196_gaa_3loop_h.pdb...<br>Read 636 atoms<br>Analyzing pdb file<br>Splitting PDB chains based on TER records or changing chain id.<br>
There are 1 chains and 0 blocks of water and 27 residues with 636 atoms<br><br> chain #res #atoms<br> 1 'A' 27 636 <br><br>WARNING: there were 55 atoms with zero occupancy and 0 atoms with<br> occupancy unequal to one (out of 636 atoms). Check your pdb file.<br>
Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/atomtypes.atp<br>Atomtype 1<br>Reading residue database... (gromos53a6)<br>Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.rtp<br>
Using default: not generating all possible dihedrals<br>Using default: excluding 3 bonded neighbors<br>Using default: generating 1,4 H--H interactions<br>Using default: removing impropers on same bond as a proper<br>Residue 108<br>
Sorting it all out...<br>Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.hdb<br>Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb<br>
Opening force field file /users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb<br><br>Back Off! I just backed up topol.top to ./#topol.top.3#<br>Processing chain 1 'A' (636 atoms, 27 residues)<br>
Identified residue DC1 as a starting terminus.<br>Identified residue DG27 as a ending terminus.<br>7 out of 7 lines of specbond.dat converted successfully<br>Warning: 'DC' not found in residue topology database, trying to use 'DCYT'<br>
Select start terminus type<br> 0: NH3+<br> 1: NH2<br> 2: None<br>2<br>Start terminus: None<br>Warning: 'DG' not found in residue topology database, trying to use 'DGUA'<br>Select end terminus type<br> 0: COO-<br>
1: COOH<br> 2: None<br>2<br>End terminus: None<br>Warning: 'DC' not found in residue topology database, trying to use 'DCYT'<br>Warning: 'DC' not found in residue topology database, trying to use 'DCYT'<br>
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DG' not found in residue topology database, trying to use 'DGUA'<br>
Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DG' not found in residue topology database, trying to use 'DGUA'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>
Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DC' not found in residue topology database, trying to use 'DCYT'<br>
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'<br>Warning: 'DA' not found in residue topology database, trying to use 'DADE'<br>Warning: 'DG' not found in residue topology database, trying to use 'DGUA'<br>
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'<br><br>-------------------------------------------------------<br>Program 452pdb2gmx, VERSION 4.5-beta2<br>Source code file: pdb2top.c, line: 887<br>
<br>Fatal error:<br>There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.<br>