I was performing protein simulation. For capping I added ACE and NH2 residues to my pdb file. I was using charmm force field , so i made changes to the rtp entry in charmm aminoacids.rtp.<div><br></div><div><div><br></div>
<div>siddhant@ubuntu:~/sura$ pdb2gmx -f bestins.pdb -o first.gro -ter</div><div> :-) G R O M A C S (-:</div><div><br></div><div> God Rules Over Mankind, Animals, Cosmos and Such</div>
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<div> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, </div><div> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, </div><div> Michael Shirts, Alfons Sijbers, Peter Tieleman,</div>
<div><br></div><div> Berk Hess, David van der Spoel, and Erik Lindahl.</div><div><br></div><div> Copyright (c) 1991-2000, University of Groningen, The Netherlands.</div><div> Copyright (c) 2001-2010, The GROMACS development team at</div>
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<div><br></div><div> :-) pdb2gmx (-:</div><div><br></div><div>Option Filename Type Description</div><div>------------------------------------------------------------</div><div>
-f bestins.pdb Input Structure file: gro g96 pdb tpr etc.</div><div> -o first.gro Output Structure file: gro g96 pdb etc.</div><div> -p topol.top Output Topology file</div><div> -i posre.itp Output Include file for topology</div>
<div> -n clean.ndx Output, Opt. Index file</div><div> -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.</div><div><br></div><div>Option Type Value Description</div><div>------------------------------------------------------</div>
<div>-[no]h bool no Print help info and quit</div><div>-[no]version bool no Print version info and quit</div><div>-nice int 0 Set the nicelevel</div><div>-chainsep enum id_or_ter Condition in PDB files when a new chain and</div>
<div> molecule_type should be started: id_or_ter,</div><div> id_and_ter, ter, id or interactive</div><div>-ff string select Force field, interactive by default. Use -h for</div>
<div> information.</div><div>-water enum select Water model to use: select, none, spc, spce,</div><div> tip3p, tip4p or tip5p</div><div>-[no]inter bool no Set the next 8 options to interactive</div>
<div>-[no]ss bool no Interactive SS bridge selection</div><div>-[no]ter bool yes Interactive termini selection, iso charged</div><div>-[no]lys bool no Interactive lysine selection, iso charged</div>
<div>-[no]arg bool no Interactive arginine selection, iso charged</div><div>-[no]asp bool no Interactive aspartic Acid selection, iso charged</div><div>-[no]glu bool no Interactive glutamic Acid selection, iso charged</div>
<div>-[no]gln bool no Interactive glutamine selection, iso neutral</div><div>-[no]his bool no Interactive histidine selection, iso checking</div><div> H-bonds</div><div>-angle real 135 Minimum hydrogen-donor-acceptor angle for a</div>
<div> H-bond (degrees)</div><div>-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)</div><div>-[no]una bool no Select aromatic rings with united CH atoms on</div>
<div> phenylalanine, tryptophane and tyrosine</div><div>-[no]ignh bool no Ignore hydrogen atoms that are in the coordinate</div><div> file</div><div>-[no]missing bool no Continue when atoms are missing, dangerous</div>
<div>-[no]v bool no Be slightly more verbose in messages</div><div>-posrefc real 1000 Force constant for position restraints</div><div>-vsite enum none Convert atoms to virtual sites: none, hydrogens</div>
<div> or aromatics</div><div>-[no]heavyh bool no Make hydrogen atoms heavy</div><div>-[no]deuterate bool no Change the mass of hydrogens to 2 amu</div><div>-[no]chargegrp bool yes Use charge groups in the .rtp file</div>
<div>-[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file)</div><div>-[no]renum bool no Renumber the residues consecutively in the output</div><div>-[no]rtpres bool no Use .rtp entry names as residue names</div>
<div><br></div><div><br></div><div>Select the Force Field:</div><div>From '/usr/share/gromacs/top':</div><div> 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)</div><div> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)</div>
<div> 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)</div><div> 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)</div><div> 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)</div>
<div> 6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)</div><div> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)</div><div> 8: CHARMM27 all-atom force field (with CMAP) - version 2.0</div>
<div> 9: GROMOS96 43a1 force field</div><div>10: GROMOS96 43a2 force field (improved alkane dihedrals)</div><div>11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)</div><div>12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)</div>
<div>13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)</div><div>14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)</div><div>15: [DEPRECATED] Encad all-atom force field, using full solvent charges</div>
<div>16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges</div><div>17: [DEPRECATED] Gromacs force field (see manual)</div><div>18: [DEPRECATED] Gromacs force field with hydrogens for NMR</div><div>
8</div><div><br></div><div>Using the Charmm27 force field in directory charmm27.ff</div><div><br></div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/watermodels.dat</div><div><br></div><div>Select the Water Model:</div>
<div> 1: TIP3P TIP 3-point, recommended</div><div> 2: TIP4P TIP 4-point</div><div> 3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS)</div><div> 4: SPC simple point charge</div><div>
5: SPC/E extended simple point charge</div><div> 6: None</div><div>1</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b</div>
<div>Reading bestins.pdb...</div><div>WARNING: all CONECT records are ignored</div><div>Read 416 atoms</div><div>Analyzing pdb file</div><div>Splitting PDB chains based on TER records or changing chain id.</div><div>WARNING: Chain identifier 'A' is used in two non-sequential blocks.</div>
<div>They will be treated as separate chains unless you reorder your file.</div><div>WARNING: Chain identifier 'A' is used in two non-sequential blocks.</div><div>They will be treated as separate chains unless you reorder your file.</div>
<div>WARNING: Chain identifier 'A' is used in two non-sequential blocks.</div><div>They will be treated as separate chains unless you reorder your file.</div><div>WARNING: Chain identifier 'A' is used in two non-sequential blocks.</div>
<div>They will be treated as separate chains unless you reorder your file.</div><div>WARNING: Chain identifier 'A' is used in two non-sequential blocks.</div><div>They will be treated as separate chains unless you reorder your file.</div>
<div>WARNING: Chain identifier 'A' is used in two non-sequential blocks.</div><div>They will be treated as separate chains unless you reorder your file.</div><div>There are 7 chains and 0 blocks of water and 55 residues with 416 atoms</div>
<div><br></div><div> chain #res #atoms</div><div> 1 ' ' 1 1 </div><div> 2 'A' 25 166 </div><div> 3 'A' 1 1 </div><div> 4 ' ' 1 2 </div><div> 5 'A' 9 67 </div>
<div> 6 ' ' 1 1 </div><div> 7 'A' 23 178 </div><div><br></div><div><br></div><div>WARNING: there were 1 atoms with zero occupancy and 18 atoms with</div><div> occupancy unequal to one (out of 416 atoms). Check your pdb file.</div>
<div><br></div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp</div><div>Atomtype 1</div><div>Reading residue database... (charmm27)</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp</div>
<div>Residue 43</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp</div><div>Residue 47</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp</div>
<div>Residue 59</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp</div><div>Residue 63</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb</div>
<div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb</div>
<div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb</div>
<div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb</div>
<div><br></div><div>Back Off! I just backed up topol.top to ./#topol.top.30#</div><div>Processing chain 1 (1 atoms, 1 residues)</div><div>There are 0 donors and 0 acceptors</div><div>There are 0 hydrogen bonds</div><div>Identified residue ACE0 as a starting terminus.</div>
<div>Identified residue ACE0 as a ending terminus.</div><div>8 out of 8 lines of specbond.dat converted successfully</div><div>Select start terminus type for ACE-0</div><div> 0: NH3+</div><div> 1: NH2</div><div> 2: None</div>
<div>2</div><div>Start terminus ACE-0: None</div><div>Select end terminus type for ACE-0</div><div> 0: COO-</div><div> 1: COOH</div><div> 2: CT2</div><div> 3: CT3</div><div> 4: None</div><div>4</div><div>End terminus ACE-0: None</div>
<div><br></div><div>-------------------------------------------------------</div><div>Program pdb2gmx, VERSION 4.5.4</div><div>Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1035</div><div><br></div>
<div>Fatal error:</div><div>T<b>here is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.</b></div><div>For more information and tips for troubleshooting, please check the GROMACS</div>
<div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div></div><div><br></div><div>I see that this problem has been listed at gmx-users list even two years back. I am using version 4.5.5-1. But still the problem is there. Can anyone help me to correctly cap the proteins.</div>
<div><br></div><div>Thanking You</div><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Siddhant Jain</blockquote>