[gmx-users] itp file problem
Anirban Ghosh
reach.anirban.ghosh at gmail.com
Mon May 7 13:56:24 CEST 2012
On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran <
bskumar.tech at gmail.com> wrote:
>
> First i had simulation of the protein alone in united atom gromacs force
> field by -ff gmx in pdb2gmx
> now i am unable to run the protein-ligand complex for the same protein
> with a ligand,
> it says the following error due to itp file generated from PRODRG,
> if i change the force field its says atom mismatch............. Please
> help me....
>
Change the force-field means? Did you change the FF with pdb2gmx, or just
in your .top file?
>
> What is the way to run the simulation
>
> grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr
> :-) G R O M A C S (-:
>
> GRoups of Organic Molecules in ACtion for Science
>
> :-) VERSION 4.0.7 (-:
>
>
> 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-4.0.7 (-:
>
> 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 prt_b4ion.pdb 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 prt.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o prt_b4ion.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 0 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'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp
> Generated 1284 of the 1485 non-bonded parameter combinations
> Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp
>
> -------------------------------------------------------
> Program grompp-4.0.7, VERSION 4.0.7
> Source code file: toppush.c, line: 947
>
> Fatal error:
> Atomtype CR1 not found
> -------------------------------------------------------
>
> "I Caught It In the Face" (P.J. Harvey)
>
>
Did you include the ligand's itp file in your .top file? I think you
haven't.
> [
>
> grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr
> :-) G R O M A C S (-:
>
> GROtesk MACabre and Sinister
>
> :-) VERSION 4.0.7 (-:
>
>
> 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-4.0.7 (-:
>
> 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 prt_b4ion.pdb 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 prt.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o prt_b4ion.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 0 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'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp
> Generated 1284 of the 1485 non-bonded parameter combinations
> Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp
> Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 3 bonded neighbours molecule type 'DRG'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file prt.top, line 18947]:
> System has non-zero total charge: -9.999978e-01
>
>
>
> processing coordinates...
>
> -------------------------------------------------------
> Program grompp-4.0.7, VERSION 4.0.7
> Source code file: grompp.c, line: 362
>
> Fatal error:
> number of coordinates in coordinate file (prt_b4ion.pdb, 79463)
> does not match topology (prt.top, 79455)
> -------------------------------------------------------
>
> "Sometimes Life is Obscene" (Black Crowes)
>
>
> --
> --
>
> *Yours Sincerely,*
> *B. Sarath Kumar, M.S (By Research),
> Tissue Culture and Drug Discovery Lab,
> Centre for Biotechnology,
> Anna University, Chennai.*
>
>
> --
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