Hi, I checked both the files they match exactly but still I get the same error message that .gro file and .top file dnt match. I dnt know how to proceed now.
Sunny On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra <[email protected]>wrote: > 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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