[gmx-users] preprocessing in position restrained step, problem with binary top file

[Xi Cheng]

Hi Moeed,

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.

Best,

Xi

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:
>
> output.grompp_pr
>
>
> *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/
> gromacs/top/ffoplsaa.itp
> 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
> charge
>   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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