[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Wed Aug 19 23:58:40 CEST 2009
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 <mishra.sunny at gmail.com>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 <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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>
>
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