[gmx-users] grompp.mdp

[abhijit kayal]

Hi,
 I am going to analyse the normal mode analysis of n-butane. For this I
donloaded a PDB id .Then opened in wordpad and just took the glu
residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make
it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created
the topology file and did the next steps .But grompp showed the following
error
abhijit at SCFBioServer project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o
ab.tp
r
                         :-)  G  R  O  M  A  C  S  (-:
                      GROwing Monsters And Cloning Shrimps
                            :-)  VERSION 4.0.4  (-:

      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.
                                :-)  grompp  (-:
Option     Filename  Type         Description
------------------------------------------------------------
  -f         em.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c         ab.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p         ab.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o         ab.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene
Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   yes     Be loud and noisy
-time        real   -1      Take frame at or first after this time.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    0       Number of allowed warnings during input
processing
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of
                            atomtypes
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 380 of the 1326 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file ab.top, line 126]:
  System has non-zero total charge: -1.000000e-00

processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 4.0.4
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (ab.gro, 13)
             does not match topology (ab.top, 29602)
-------------------------------------------------------
"A Lady Shaves Her Legs" (C. Meijering)
                              So my questioin is my way of procedding is
wrong or right?
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