[gmx-users] pdb2gmx error
Alpay Temiz
alpay.temiz at gmail.com
Thu Aug 12 16:30:53 CEST 2010
Hello everyone
I am trying to set up a nucleic acid only simulation using gromacs 4.5.2
pdb2gmx is giving me only options to cap protein terminals and when I choose
none it gives the error:
"There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry."
and exits.
below is the program output.
Alpay
452pdb2gmx -f chr13_115016196_gaa_3loop_h.pdb -o conf.pdb -p -inter
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.5-beta2 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
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.
:-) 452pdb2gmx (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f chr13_115016196_gaa_3loop_h.pdb Input Structure file: gro g96
pdb tpr etc.
-o conf.pdb 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
-[no]cwd bool no Also read force field files from the current
working directory
-[no]rtpo bool no Allow an entry in a local rtp file to override a
library rtp entry
-chainsep enum id_or_ter Condition in PDB files when a new chain
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 yes Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
-[no]arg bool no Interactive Arganine 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 pdb 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:
1: AMBER03_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
2: AMBER94_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
3: AMBER96_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
4: AMBER99_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
5: AMBER99SB-ILDN_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
6: AMBER99SB_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
7: AMBERGS_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION
8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta
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
13
Using the Gromos53a6 force field in directory
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/watermodels.dat
Select the Water Model:
1: SPC simple point charge, recommended
2: SPC/E extended simple point charge
3: None
1
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading chr13_115016196_gaa_3loop_h.pdb...
Read 636 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 27 residues with 636 atoms
chain #res #atoms
1 'A' 27 636
WARNING: there were 55 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 636 atoms). Check your pdb file.
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file
/users/n2000546794/temizna/gromacs.4.5.b2/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 'A' (636 atoms, 27 residues)
Identified residue DC1 as a starting terminus.
Identified residue DG27 as a ending terminus.
7 out of 7 lines of specbond.dat converted successfully
Warning: 'DC' not found in residue topology database, trying to use 'DCYT'
Select start terminus type
0: NH3+
1: NH2
2: None
2
Start terminus: None
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
Select end terminus type
0: COO-
1: COOH
2: None
2
End terminus: None
Warning: 'DC' not found in residue topology database, trying to use 'DCYT'
Warning: 'DC' not found in residue topology database, trying to use 'DCYT'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DC' not found in residue topology database, trying to use 'DCYT'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
-------------------------------------------------------
Program 452pdb2gmx, VERSION 4.5-beta2
Source code file: pdb2top.c, line: 887
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
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