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
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