[gmx-users] .top file from .gro file
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 20 00:09:53 CEST 2009
sunny mishra wrote:
> 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.
>
Well, something has to be wrong, or else grompp wouldn't complain. You say
you've checked the .top, but have you also checked the contents of any relevant
.itp files that are #included within it?
-Justin
> Sunny
>
> On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra <mishra.sunny at gmail.com
> <mailto: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 <mailto: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
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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 gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list