The useful part of the error file
-f em.mdp Inputgrompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c filled_box.pdb InputStructure 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 InputTopology 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: 0.98
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 InputRun input file: tpr tpb tpa
-tabletable.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
-potpot.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
-niceint19 Set the nicelevel
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-np int0 Number of positive ions
-pname string NA Name of the positive ion
-pq int1 Charge of the positive ion
-nn int2 Number of negative ions
-nname string CL Name of the negative ion
-nq int-1 Charge of the negative ion
-rminreal 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
-seedint1993Seed for random number generator
-scale real 0.001 Scaling factor for the potential for -pot
-concreal 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
Group10 (Prot-Masses) has 4072 elements
Group11 (non-Protein) has 46702 elements
Group12 ( Other) has 3 elements
Group13 (AZI) has 3 elements
Group14 ( ZN) has 1 elements
Group15 (Ion) has 1 elements
Group16 (AZI) has 3 elements
Group17 ( ZN) has 1 elements
Group18 ( Water) has 46698 elements
Group19 (SOL) has 46698 elements
