Hi,
I am going to analyse the normal mode analysis of n-butane. For this I
donloaded a PDB id .Then opened in wordpad and just took the glu
residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make
it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created
the topology file and did the next steps .But grompp showed the following
error
abhi...@scfbioserver project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o
ab.tp
r
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) VERSION 4.0.4 (-:
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 ab.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 ab.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o ab.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 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 380 of the 1326 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.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'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file ab.top, line 126]:
System has non-zero total charge: -1.000000e-00
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 4.0.4
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (ab.gro, 13)
does not match topology (ab.top, 29602)
-------------------------------------------------------
"A Lady Shaves Her Legs" (C. Meijering)
So my questioin is my way of procedding is
wrong or right?
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