[gmx-users] .top file from .gro file

[Mark Abraham]

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