[gmx-users] cannot generate .top file

Kwee Hong joyssstan0202 at gmail.com
Fri Oct 24 10:41:59 CEST 2008

I seem having some problem in running ./pdb2gmx. Here is the output file.
Can you help me in giving me some idea to deal with this?

bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro
                         :-)  G  R  O  M  A  C  S  (-:

        Getting the Right Output Means no Artefacts in Calculating Stuff

                            :-)  VERSION 3.3.3  (-:

      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.

                               :-)  pdb2gmx  (-:

Option     Filename  Type         Description
  -f       1aml.pdb  Input        Generic structure: gro g96 pdb tpr tpb tpa
  -o       1aml.gro  Output       Generic structure: gro g96 pdb xml
  -p       1aml.top  Output       Topology file
  -i      posre.itp  Output       Include file for topology
  -n      clean.ndx  Output, Opt. Index file
  -q      clean.pdb  Output, Opt. Generic structure: gro g96 pdb xml

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-nice        int    0       Set the nicelevel
-[no]merge   bool   no      Merge chains into one molecule definition
-ff          string select  Force field, interactive by default. Use -h for
-water       enum   spc     Water model to use: with GROMOS we recommend
                            with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p
                            or f3c
-[no]inter   bool   no      Set the next 6 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
-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
-[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

Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43b1 vacuum force field
 2: GROMOS96 43a2 force field (improved alkane dihedrals)
 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 7: Encad all-atom force field, using scaled-down vacuum charges
 8: Encad all-atom force field, using full solvent charges
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Reading 1aml.pdb...
Read 'AMYLOID A4', 598 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 40 residues with 598 atoms

  chain  #res #atoms
  1 ' '    40    598

All occupancies are one
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.atp
Atomtype 50
Reading residue database... (ffG43a2)
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-c.tdb

Program pdb2gmx, VERSION 3.3.3
Source code file: futil.c, line: 313

File input/output error:

I seem to be having problem in running the test tun as well. Below is its

bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl
Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex |
kernel | pdb2gmx | all ]
   or: ./gmxtest.pl clean | refclean | dist


Best regards,
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