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On 4/27/2011 6:21 AM, delara aghaie wrote:
<blockquote cite="mid:578999.34299.qm@web130106.mail.mud.yahoo.com"
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<div>Dear Gromacs users</div>
<div>I ahve a dppc monolayer on water layer 9tip4p-2005).
I have added 8 Mg and 16 Cl ions using genion and now
want to use grompp and then start the simulation to see
the effect of ions on the pressure-area isotherm of the
system.</div>
<div> </div>
<div>running grompp in gromacs 3.3 I see he following
error:</div>
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<br>
Unless you have an important reason of continuity for using GROMACS
3.3, you will get much better performance from the latest GROMACS
version.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:578999.34299.qm@web130106.mail.mud.yahoo.com"
type="cite">
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<div>please help em to solve it.let me knoe please what is
cpp?</div>
<div>Thanks in advance</div>
<div>D. Aghaie</div>
<div> </div>
<div>-bash-3.2$ <font color="#c00000">grompp_mpi -c
dppc-salt-Mg-0.1.gro -f run.mdp -n indexsalt-Mg.ndx -p
topoldppc.top -o topol.tpr -np 8<br>
</font> <font color="#00007f">:-)
G R O M A C S (-:</font></div>
<div><font color="#00007f"> Groningen
Machine for Chemical Simulation</font></div>
<div><font color="#00007f">
:-) VERSION 3.3 (-:</font></div>
<div><br>
<font color="#00007f"> 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) 2001-2004, The GROMACS
development team,<br>
check out </font><a
moz-do-not-send="true" href="http://www.gromacs.org"><font
color="#00007f">http://www.gromacs.org</font></a><font
color="#00007f"> for more information.</font></div>
<div><font color="#00007f"> 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.</font></div>
<div><font color="#00007f">
:-) grompp_mpi (-:</font></div>
<div><font color="#00007f">Option Filename
Type Description<br>
------------------------------------------------------------<br>
-f run.mdp Input, Opt! grompp input file
with MD parameters<br>
-po mdout.mdp Output grompp input file
with MD parameters<br>
-c dppc-salt-Mg-0.1.gro Input Generic
structure: gro g96 pdb tpr<br>
tpb tpa xml<br>
-r conf.gro Input, Opt. Generic structure:
gro g96 pdb tpr tpb tpa<br>
xml<br>
-rb conf.gro Input, Opt. Generic structure:
gro g96 pdb tpr tpb tpa<br>
xml<br>
-n indexsalt-Mg.ndx Input, Opt! Index file<br>
-deshuf deshuf.ndx Output, Opt. Index file<br>
-p topoldppc.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br>
-o topol.tpr Output Generic run input:
tpr tpb tpa xml<br>
-t traj.trr Input, Opt. Full precision
trajectory: trr trj<br>
-e ener.edr Input, Opt. Generic energy: edr
ene</font></div>
<div><font color="#00007f"> Option Type Value
Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]X bool no Use dialog box GUI to edit
command line options<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>
-np int 8 Generate statusfile for #
nodes<br>
-[no]shuffle bool no Shuffle molecules over
nodes<br>
-[no]sort bool no Sort molecules according
to X coordinate<br>
-[no]rmvsbds bool yes Remove constant bonded
interactions with virtual<br>
sites<br>
-load string Releative load capacity of
each node on a<br>
parallel machine. Be sure
to use quotes around<br>
the string, which should
contain a number for<br>
each node<br>
-maxwarn int 10 Number of warnings after
which input processing<br>
stops<br>
-[no]check14 bool no Remove 1-4 interactions
without Van der Waals<br>
-[no]renum bool yes Renumber atomtypes and
minimize number of<br>
atomtypes</font></div>
<div><font color="#00007f">creating statusfile for 8
nodes...</font></div>
<div><font color="#00007f">Back Off! I just backed up
mdout.mdp to ./#mdout.mdp.1#<br>
checking input for internal consistency...<br>
<font color="#407f00">calling cpp...<br>
topoldppc.top:7:20: error: ions.itp: No such file or
directory<br>
cpp exit code: 256<br>
Tried to execute: 'cpp
-I/apps/gromacs/3.3/share/top topoldppc.top >
gromppzVWhWp'<br>
The 'cpp' command is defined in the .mdp file<br>
processing topology...<br>
Generated 1369 of the 2211 non-bonded parameter
combinations<br>
Excluding 3 bonded neighbours for DPP 64<br>
turning all bonds into constraints...<br>
Excluding 2 bonded neighbours for SOL 4152<br>
turning all bonds into constraints...<br>
Cleaning up temporary file gromppzVWhWp<br>
</font>-------------------------------------------------------<br>
Program grompp_mpi, VERSION 3.3<br>
Source code file: toppush.c, line: 1264</font></div>
<div><font color="#00007f"><font color="#7f003f">Fatal
error:<br>
No such moleculetype Mg<br>
</font>-------------------------------------------------------</font></div>
<div><font color="#00007f">Thanx for Using GROMACS - Have
a Nice Day</font></div>
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