Ok..I will see that and let you know. Thanks for the help though. Sunny On Tue, Aug 18, 2009 at 8:12 PM, Mark Abraham <[email protected]>wrote:
> sunny mishra wrote: > >> I did the same but again i get the same error..something like this >> >> awk -f atom2cg_v2.1tryout.awk 1K4C.pdb > 1K4C_cg.pdb >> >> (This generated 1K4C_cg.pdb file) >> >> genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro >> >> (produced 1K4C_cg.gro) >> >> GROningen MAchine for Chemical Simulation >> >> :-) VERSION 4.0.5 (-: >> >> >> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2008, The GROMACS development team, >> check out http://www.gromacs.org for more information. >> >> This program is free software; you can redistribute it and/or >> modify it under the terms of the GNU General Public License >> as published by the Free Software Foundation; either version 2 >> of the License, or (at your option) any later version. >> >> :-) genbox (-: >> >> Option Filename Type Description >> ------------------------------------------------------------ >> -cp 1K4C_cg.pdb Input, Opt! Structure file: gro g96 pdb tpr tpb tpa >> -cs spc216.gro Input, Opt., Lib. Structure file: gro g96 pdb tpr tpb >> tpa >> -ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr tpb >> tpa >> -o 1K4C_cg.gro Output Structure file: gro g96 >> pdb >> -p topol.top In/Out, Opt. Topology >> file >> >> Option Type Value Description >> ------------------------------------------------------ >> -[no]h bool no Print help info and quit >> -nice int 19 Set the nicelevel >> -box vector 10 10 10 box size >> -nmol int 0 no of extra molecules to insert >> -try int 10 try inserting -nmol*-try times >> -seed int 1997 random generator seed >> -vdwd real 0.105 default vdwaals distance >> -shell real 0 thickness of optional water layer around >> solute >> -maxsol int 0 maximum number of solvent molecules to add if >> they fit in the box. If zero (default) this is >> ignored >> -[no]vel bool no keep velocities from input solute and solvent >> >> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >> WARNING: masses will be determined based on residue and atom names, >> this can deviate from the real mass of the atom type >> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat >> Entries in atommass.dat: 178 >> WARNING: vdwradii will be determined based on residue and atom names, >> this can deviate from the real mass of the atom type >> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat >> Entries in vdwradii.dat: 28 >> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat >> Entries in dgsolv.dat: 7 >> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat >> Entries in electroneg.dat: 71 >> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat >> Entries in elements.dat: 218 >> Reading solute configuration >> MEMBRANE PROTEIN >> Containing 1127 atoms in 534 residues >> Initialising van der waals distances... >> Writing generated configuration to 1K4C_cg.gro >> MEMBRANE PROTEIN >> >> Output configuration contains 1127 atoms in 534 residues >> Volume : 1000 (nm^3) >> Density : 53.8545 (g/l) >> Number of SOL molecules: 0 >> >> >> gcq#69: "I Want to Know Right Now" (Meatloaf) >> >> >> After that ;;;;;;;;;;;;;;;;;;;;;;; >> >> grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10 >> >> :-) G R O M A C S >> (-: >> >> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon >> >> :-) VERSION 4.0.5 (-: >> >> >> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2008, The GROMACS development team, >> check out http://www.gromacs.org for more information. >> >> This program is free software; you can redistribute it and/or >> modify it under the terms of the GNU General Public License >> as published by the Free Software Foundation; either version 2 >> of the License, or (at your option) any later version. >> >> :-) grompp (-: >> >> Option Filename Type Description >> ------------------------------------------------------------ >> -f em.mdp Input, Opt! grompp input file with MD parameters >> -po mdout.mdp Output grompp input file with MD parameters >> -c 1K4C_cg.gro Input Structure file: gro g96 pdb tpr tpb tpa >> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa >> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa >> -n index.ndx Input, Opt. Index file >> -p 1K4C.top Input Topology file >> -pp processed.top Output, Opt. Topology file >> -o topol.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: edr ene >> >> Option Type Value Description >> ------------------------------------------------------ >> -[no]h bool no Print help info and quit >> -nice int 0 Set the nicelevel >> -[no]v bool yes Be loud and noisy >> -time real -1 Take frame at or first after this time. >> -[no]rmvsbds bool yes Remove constant bonded interactions with >> virtual >> sites >> -maxwarn int 10 Number of allowed warnings during input >> processing >> -[no]zero bool no Set parameters for bonded interactions >> without >> defaults to zero instead of generating an >> error >> -[no]renum bool yes Renumber atomtypes and minimize number >> of >> >> atomtypes >> >> Ignoring obsolete mdp entry 'title' >> Ignoring obsolete mdp entry 'cpp' >> Replacing old mdp entry 'unconstrained_start' by 'continuation' >> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9# >> checking input for internal consistency... >> >> NOTE 1 [file em.mdp, line unknown]: >> For energy conservation with switch/shift potentials, rlist should be 0.1 >> to 0.3 nm larger than rcoulomb. >> >> >> NOTE 2 [file em.mdp, line unknown]: >> For energy conservation with switch/shift potentials, rlist should be 0.1 >> to 0.3 nm larger than rvdw. >> >> processing topology... >> Generated 0 of the 465 non-bonded parameter combinations >> Excluding 1 bonded neighbours molecule type 'Protein' >> >> NOTE 3 [file 1K4C.top, line 15]: >> System has non-zero total charge: 4.000000e+00 >> >> >> >> processing coordinates... >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.0.5 >> Source code file: grompp.c, line: 362 >> >> Fatal error: >> number of coordinates in coordinate file (1K4C_cg.gro, 1127) >> does not match topology (1K4C.top, 1166) >> ------------------------------------------------------- >> > > That's a pretty explicit error message. Go and look at the molecule and > atom ordering in the two files and see where they don't match. > > Mark > > _______________________________________________ > 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 >
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