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 <[email protected]> > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
