<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><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>
<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 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></td></tr></table>