[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
> --
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