[gmx-users] Re: Genion cannot read from input

[Nathan Bullock]

The useful part of the error file

------------------------------------------------------------
  -f         em.mdp  Input        grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c filled_box.pdb  Input        Structure file: gro g96 pdb tpr etc.
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n      index.ndx  Input, Opt.  Index file
  -p protein_mod_filled5.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o       ions.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
Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
Generated 2415 of the 2415 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2415 of the 2415 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'AZI'
Excluding 1 bonded neighbours molecule type 'ZN'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file protein_mod_filled5.top, line 38757]:
  System has non-zero total charge: 0.999998
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
 
Number of degrees of freedom in T-Coupling group rest is 105621.00
Estimate for the relative computational load of the PME mesh part: 0.27

There was 1 note

Back Off! I just backed up ions.tpr to ./#ions.tpr.6#
/usr/local/gromacs-4.5.5/bin/genion  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s       ions.tpr  Input        Run input file: tpr tpb tpa
-table    table.xvg  Input, Opt.  xvgr/xmgr file
  -n      index.ndx  Input, Opt.  Index file
  -o  solv_ions.pdb  Output       Structure file: gro g96 pdb etc.
  -g     genion.log  Output       Log file
-pot        pot.pdb  Output, Opt. Protein data bank file
  -p protein_mod_filled5.top  In/Out, Opt! Topology file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    19      Set the nicelevel
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-np          int    0       Number of positive ions
-pname       string NA      Name of the positive ion
-pq          int    1       Charge of the positive ion
-nn          int    2       Number of negative ions
-nname       string CL      Name of the negative ion
-nq          int    -1      Charge of the negative ion
-rmin        real   0.6     Minimum distance between ions
-[no]random  bool   yes     Use random placement of ions instead of based on
                            potential. The rmin option should still work
-seed        int    1993    Seed for random number generator
-scale       real   0.001   Scaling factor for the potential for -pot
-conc        real   0       Specify salt concentration (mol/liter). This
will
                            add sufficient ions to reach up to the specified
                            concentration as computed from the volume of the
                            cell in the input .tpr file. Overrides the -np
                            and -nn options.
-[no]neutral bool   no      This option will add enough ions to neutralize
                            the system. In combination with the
concentration
                            option a neutral system at a given salt
                            concentration will be generated.


Back Off! I just backed up genion.log to ./#genion.log.6#
Reading file ions.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Group     0 (         System) has 50774 elements
Group     1 (        Protein) has  4072 elements
Group     2 (      Protein-H) has  2059 elements
Group     3 (        C-alpha) has   258 elements
Group     4 (       Backbone) has   774 elements
Group     5 (      MainChain) has  1033 elements
Group     6 (   MainChain+Cb) has  1269 elements
Group     7 (    MainChain+H) has  1276 elements
Group     8 (      SideChain) has  2796 elements
Group     9 (    SideChain-H) has  1026 elements
Group    10 (    Prot-Masses) has  4072 elements
Group    11 (    non-Protein) has 46702 elements
Group    12 (          Other) has     3 elements
Group    13 (            AZI) has     3 elements
Group    14 (             ZN) has     1 elements
Group    15 (            Ion) has     1 elements
Group    16 (            AZI) has     3 elements
Group    17 (             ZN) has     1 elements
Group    18 (          Water) has 46698 elements
Group    19 (            SOL) has 46698 elements
Group    20 (      non-Water) has  4076 elements
Group    21 ( Water_and_ions) has 46699 elements
Select a group: 
-------------------------------------------------------
Program genion, VERSION 4.5.5
Source code file: index.c, line: 1036

Fatal error:
Cannot read from input



-----
Graduate Student
University of Iowa 
Cheatum Research Group
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