[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Wed Aug 19 02:18:48 CEST 2009
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 <Mark.Abraham at anu.edu.au>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
>
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