Hi Ankita ,
The error is self-explanatory , and simple to interpret it.
You check the Topology file and see the last line that showing
added ions ...
What was your genion COMMAND LINE........????
Have a nice day
Rama
On Mon, Apr 2, 2012 at 3:19 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote:
>
> 2 apr 2012 kl. 11.27 skrev ankita oindrila:
>
> We are trying to do simulation of lysozyme in water.
>
> step with problem : energy minimization.
>
> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>
> :-) G R O M A C S (-:
>
> Getting the Right Output Means no Artefacts in Calculating Stuff
>
> :-) 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 minim.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c 1AKI_solv_ions.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 topol.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o em.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
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5
> Source code file: toppush.c, line: 1641
>
> Fatal error:
> No such moleculetype NA
>
> what should we do????
>
>
> Have a look at http://www.gromacs.org/Documentation/Errors
>
>
>
> --
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
> --
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