sunny mishra wrote:
Hi,
I checked both the files they match exactly but still I get the same
error message that .gro file and .top file dnt match. I dnt know how to
proceed now.
Well, something has to be wrong, or else grompp wouldn't complain. You say
you've checked the .top, but have you also checked the contents of any relevant
.itp files that are #included within it?
-Justin
Sunny
On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra <[email protected]
<mailto:[email protected]>> wrote:
Ok..I will see that and let you know. Thanks for the help though.
Sunny
On Tue, Aug 18, 2009 at 8:12 PM, Mark Abraham
<[email protected] <mailto:[email protected]>> wrote:
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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