[gmx-users] Error_message

[pkmukher]

Hi,

  I am trying to generate a .tpr file for my ligand and I am
getting the follwing error message.I would be greatful if
somebody could look into it and tell me what the errors
are.Thanks

r1028 at redwood:~/gromacs/drugenz2/junk> grompp -f em.mdp -c
trp_b4ion.pdb -p trp.top -o trp_b4ion.tpr -nice 1
                         :-)  G  R  O  M  A  C  S  (-:

             Gallium Rubidium Oxygen Manganese Argon Carbon
Silicon

                            :-)  VERSION 3.3.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk
Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
             Copyright (c) 2001-2006, 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  trp_b4ion.pdb  Input        Generic structure: gro g96
pdb tpr tpb tpa
                                   xml
  -r       conf.gro  Input, Opt.  Generic structure: gro g96
pdb tpr tpb tpa
                                   xml
 -rb       conf.gro  Input, Opt.  Generic structure: gro g96
pdb tpr tpb tpa
                                   xml
  -n      index.ndx  Input, Opt.  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p        trp.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o  trp_b4ion.tpr  Output       Generic run input: tpr tpb
tpa xml
  -t       traj.trr  Input, Opt.  Full precision trajectory:
trr trj
  -e       ener.edr  Input, Opt.  Generic energy: edr ene

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
       -nice    int      1  Set the nicelevel
      -[no]v   bool    yes  Be loud and noisy
       -time   real     -1  Take frame at or first after
this time.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X
coordinate
-[no]rmvsbds   bool    yes  Remove constant bonded
interactions with virtual
                            sites
       -load string         Releative load capacity of each
node on a
                            parallel machine. Be sure to use
quotes around
                            the string, which should contain
a number for
                            each node
    -maxwarn    int     10  Number of warnings after which
input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without
Van der Waals
  -[no]renum   bool    yes  Renumber atomtypes and minimize
number of
                            atomtypes

creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
'l-bfgs' 'tpi'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds'
'h-angles' 'all-angles'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 3 bonded neighbours for IN4 1
Excluding 2 bonded neighbours for SOL 4778
NOTE:
  System has non-zero total charge: 9.000002e+00

processing coordinates...
double-checking input for internal consistency...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 1109

Fatal error:
There were 4 error(s) processing your input
-------------------------------------------------------

"Encountered Subspace Anomaly" (Star Trek)


Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286