[gmx-users] Capping error in pdb2gmx

siddhant jain siddhantjain92 at gmail.com
Sun Jun 10 14:19:11 CEST 2012


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 at ubuntu:~/sura$ pdb2gmx -f bestins.pdb -o first.gro -ter
                         :-)  G  R  O  M  A  C  S  (-:

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                            :-)  VERSION 4.5.4  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
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        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

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         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.

Thanking You

> Siddhant Jain
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