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

Warren Gallin wgallin at ualberta.ca
Sat Apr 27 23:22:07 CEST 2013


The problem is that genion is expecting input from the command line, telling it which molecules to replace with ions - usually SOL.

If you are running a script you have to script an input line for genion.

Warren Gallin

On 2013-04-27, at 2:56 PM, Nathan Bullock <bullocknathan534 at gmail.com> wrote:

> 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
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Genion-cannot-read-from-input-tp5007724p5007733.html
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