[gmx-users] preprocessing in position restrained step, problem with binary top file
cx19871012 at gmail.com
Thu Jun 17 07:38:08 CEST 2010
Hello, I use to encounter the same error and I fix it by modifying the index
file (.ndx). Maybe you have re-define the group name in your topology file.
You can have a check on the .ndx file and see if *protein *has been
included. I do it like first,
make_ndx -f *.gro -o *.ndx
then modify it by command or manually change the content of *.ndx file.
Hope this could help, good luck.
2010/4/25 Moeed <lecielll at googlemail.com>
> I would be most thankful if you could help me warning 1, note 1 and thr
> fatal error. I I read about -n option but I dont know where in command line
> i have to include it. Thank you.
> grompp -f pr -c Hexane_b4pr.gro -r Hexane_b4pr.gro -p HexaneModified-Residuename.top -o Hexane_pr >& output.grompp_pr
> output file:
> *WARNING 1 [file pr.mdp, line unknown]:
> Unknown or double left-hand 'warnings' in parameter file*
> checking input for internal consistency...
> *NOTE 1 [file pr.mdp, line unknown]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat.
> Opening library file /chem_soft/gromacs/share/
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'HEX'
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> renumbering atomtypes...
> converting bonded parameters...
> NOTE 2 [file HexaneModified-Residuename.top, line unknown]:
> The largest charge group contains 20 atoms.
> Since atoms only see each other when the centers of geometry of the
> groups they belong to are within the cut-off distance, too large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> initialising group options...
> processing index file...
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> Program grompp, VERSION 4.0.7
> Source code file: readir.c, line: 1007
> *Fatal error:
> Group protein not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the '-n'
> option of grompp.
> In that case use the '-n' option.
> pr.mdp file:*************************************************************
> warnings = 10
> cpp = /lib/cpp
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 500 ; total 1.0 ps.
> nstcomm = 1
> nstxout = 10
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc-grps = protein sol
> ref_t = 300 300
> ; Pressure coupling is not on
> Pcoupl = no
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
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