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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
