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