Ok..I will see that and let you know. Thanks for the help though.<div><br></div><div>Sunny<br><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 8:12 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5">sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I did the same but again i get the same error..something like this<br>
<br>
awk -f atom2cg_v2.1tryout.awk 1K4C.pdb > 1K4C_cg.pdb<br>
<br>
(This generated 1K4C_cg.pdb file)<br>
<br>
genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro<br>
<br>
(produced 1K4C_cg.gro)<br>
<br>
GROningen MAchine for Chemical Simulation<br>
<br>
:-) VERSION 4.0.5 (-:<br>
<br>
<br>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a> for more information.<br>
<br>
This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br>
as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br>
<br>
:-) genbox (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-cp 1K4C_cg.pdb Input, Opt! Structure file: gro g96 pdb tpr tpb tpa<br>
-cs spc216.gro Input, Opt., Lib. Structure file: gro g96 pdb tpr tpb<br>
tpa<br>
-ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr tpb<br>
tpa<br>
-o 1K4C_cg.gro Output Structure file: gro g96<br>
pdb<br>
-p topol.top In/Out, Opt. Topology<br>
file<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-nice int 19 Set the nicelevel<br>
-box vector 10 10 10 box size<br>
-nmol int 0 no of extra molecules to insert<br>
-try int 10 try inserting -nmol*-try times<br>
-seed int 1997 random generator seed<br>
-vdwd real 0.105 default vdwaals distance<br>
-shell real 0 thickness of optional water layer around solute<br>
-maxsol int 0 maximum number of solvent molecules to add if<br>
they fit in the box. If zero (default) this is<br>
ignored<br>
-[no]vel bool no keep velocities from input solute and solvent<br>
<br>
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat<br>
Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat<br>
Entries in vdwradii.dat: 28<br>
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>
Entries in electroneg.dat: 71<br>
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>
Entries in elements.dat: 218<br>
Reading solute configuration<br>
MEMBRANE PROTEIN<br>
Containing 1127 atoms in 534 residues<br>
Initialising van der waals distances...<br>
Writing generated configuration to 1K4C_cg.gro<br>
MEMBRANE PROTEIN<br>
<br>
Output configuration contains 1127 atoms in 534 residues<br>
Volume : 1000 (nm^3)<br>
Density : 53.8545 (g/l)<br>
Number of SOL molecules: 0<br>
<br>
<br>
gcq#69: "I Want to Know Right Now" (Meatloaf)<br>
<br>
<br>
After that ;;;;;;;;;;;;;;;;;;;;;;;<br>
<br>
grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10<br>
<br>
:-) G R O M A C S<br>
(-:<br>
<br>
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon<br>
<br>
:-) VERSION 4.0.5 (-:<br>
<br>
<br>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a> for more information.<br>
<br>
This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br>
as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br>
<br>
:-) grompp (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f em.mdp Input, Opt! grompp input file with MD parameters<br>
-po mdout.mdp Output grompp input file with MD parameters<br>
-c 1K4C_cg.gro Input Structure file: gro g96 pdb tpr tpb tpa<br>
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-n index.ndx Input, Opt. Index file<br>
-p 1K4C.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br>
-o topol.tpr Output Run input file: tpr tpb tpa<br>
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
-e ener.edr Input, Opt. Energy file: edr ene<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-nice int 0 Set the nicelevel<br>
-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br>
sites<br>
-maxwarn int 10 Number of allowed warnings during input<br>
processing<br>
-[no]zero bool no Set parameters for bonded interactions<br>
without<br>
defaults to zero instead of generating an<br>
error<br>
-[no]renum bool yes Renumber atomtypes and minimize number<br>
of<br>
<br>
atomtypes<br>
<br>
Ignoring obsolete mdp entry 'title'<br>
Ignoring obsolete mdp entry 'cpp'<br>
Replacing old mdp entry 'unconstrained_start' by 'continuation'<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#<br>
checking input for internal consistency...<br>
<br>
NOTE 1 [file em.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be 0.1<br>
to 0.3 nm larger than rcoulomb.<br>
<br>
<br>
NOTE 2 [file em.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be 0.1<br>
to 0.3 nm larger than rvdw.<br>
<br>
processing topology...<br>
Generated 0 of the 465 non-bonded parameter combinations<br>
Excluding 1 bonded neighbours molecule type 'Protein'<br>
<br>
NOTE 3 [file 1K4C.top, line 15]:<br>
System has non-zero total charge: 4.000000e+00<br>
<br>
<br>
<br>
processing coordinates...<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.5<br>
Source code file: grompp.c, line: 362<br>
<br>
Fatal error:<br>
number of coordinates in coordinate file (1K4C_cg.gro, 1127)<br>
does not match topology (1K4C.top, 1166)<br>
-------------------------------------------------------<br>
</blockquote>
<br></div></div>
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.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br></div>