*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????
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
