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

[Moeed]

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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