[gmx-users] pdb2gmx stop at "AtomType 1"

英雄不再寂寞 xiaowu759 at qq.com
Sat Oct 16 12:38:49 CEST 2010

Dear gmx-users,
   I have added the required residue groups in the rtp file. Then I run the pdb2gmx using the following line for the top file, only to stop at " AtomType 1". No any message is given. I can not think out what is happening at all. Please help me with this problem, thanks a lot. Note that I am using gmx-4.5.
   Chaofu Wu, Dr.
 xiaowu759 at linux-s38y:~/workshop> pdb2gmx -f deta.pdb -o deta.gro -p deta.top -i deta.itp -ter
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                                :-)  pdb2gmx  (-:
 Option     Filename  Type         Description
  -f       deta.pdb  Input        Structure file: gro g96 pdb tpr etc.
  -o       deta.gro  Output       Structure file: gro g96 pdb etc.
  -p       deta.top  Output       Topology file
  -i       deta.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
-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 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
-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:
From current directory:
 1: CNT_OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 2: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
From '/usr/local/gromacs/share/gromacs/top':
 3: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 4: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 5: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 6: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 7: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
 8: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
 9: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
10: CHARMM27 all-atom force field (with CMAP) - version 2.0beta
11: GROMOS96 43a1 force field
12: GROMOS96 43a2 force field (improved alkane dihedrals)
13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
17: [DEPRECATED] Encad all-atom force field, using full solvent charges
18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
19: [DEPRECATED] Gromacs force field (see manual)
20: [DEPRECATED] Gromacs force field with hydrogens for NMR
 Using the Oplsaa force field in directory oplsaa.ff
 Opening force field file oplsaa.ff/watermodels.dat
 Select the Water Model:
 1: TIP4P  TIP 4-point, recommended
 2: TIP3P  TIP 3-point
 3: TIP5P  TIP 5-point
 4: SPC    simple point charge
 5: SPC/E  extended simple point charge
 6: None
Opening force field file oplsaa.ff/aminoacids.r2b
Reading deta.pdb...
Read 20 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 1 residues with 20 atoms
   chain  #res #atoms
  1 ' '     1     20  
 All occupancies are one
Opening force field file oplsaa.ff/atomtypes.atp
Atomtype 1
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