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 <bullocknathan...@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 > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. 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