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I got the same error when doing the lysozyme tutorial on one of the machines provided by NERSC.<BR>
the dept. of energy provided high performance computing service, specifically the carver machine.<BR>
<BR>
The gromacs default on that machine I think is also 3.*.*, so I'll go with the "former" also, namely #include statement.<BR>
<BR>
v/r,<BR>
<BR>
dc<BR> <BR>
> Date: Tue, 26 Apr 2011 16:23:52 -0400<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: [gmx-users] Re: error when running grompp<BR>> <BR>> <BR>> <BR>> delara aghaie wrote:<BR>> > Dear Gromacs users<BR>> > I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg <BR>> > and 16 Cl ions using genion and now want to use grompp and then start <BR>> > the simulation to see the effect of ions on the pressure-area isotherm <BR>> > of the system.<BR>> > <BR>> > running grompp in gromacs 3.3 I see he following error:<BR>> > please help em to solve it.let me knoe please what is cpp?<BR>> <BR>> The C-preprocessor. In ancient Gromacs versions like this one, it was needed to <BR>> interpret include, define, ifdef, etc.<BR>> <BR>> Your main problem is this:<BR>> <BR>> > topoldppc.top:7:20: error: ions.itp: No such file or directory<BR>> <BR>> which then results in:<BR>> <BR>> > -------------------------------------------------------<BR>> > Program grompp_mpi, VERSION 3.3<BR>> > Source code file: toppush.c, line: 1264<BR>> > Fatal error:<BR>> > No such moleculetype Mg<BR>> > -------------------------------------------------------<BR>> > Thanx for Using GROMACS - Have a Nice Day<BR>> > <BR>> <BR>> Either your #include statement in your .top is wrong or your cpp is <BR>> nonfunctional, but I suspect the former.<BR>> <BR>> -Justin<BR>> <BR>> -- <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Ph.D. Candidate<BR>> ICTAS Doctoral Scholar<BR>> MILES-IGERT Trainee<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul[at]vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> <BR>> ========================================<BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR> </body>
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