[gmx-users] Re: error when running grompp

[Daniel Casimir]

I got the same error when doing the lysozyme tutorial on one of the machines provided by NERSC.
the dept. of energy provided high performance computing service, specifically the carver machine.
 
The gromacs default on that machine I think is also 3.*.*, so I'll go with the "former" also, namely #include statement.
 
v/r,
 
dc
 
> Date: Tue, 26 Apr 2011 16:23:52 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: error when running grompp
> 
> 
> 
> delara aghaie wrote:
> > Dear Gromacs users
> > 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.
> > 
> > running grompp in gromacs 3.3 I see he following error:
> > please help em to solve it.let me knoe please what is cpp?
> 
> The C-preprocessor. In ancient Gromacs versions like this one, it was needed to 
> interpret include, define, ifdef, etc.
> 
> Your main problem is this:
> 
> > topoldppc.top:7:20: error: ions.itp: No such file or directory
> 
> which then results in:
> 
> > -------------------------------------------------------
> > Program grompp_mpi, VERSION 3.3
> > Source code file: toppush.c, line: 1264
> > Fatal error:
> > No such moleculetype Mg
> > -------------------------------------------------------
> > Thanx for Using GROMACS - Have a Nice Day
> > 
> 
> Either your #include statement in your .top is wrong or your cpp is 
> nonfunctional, but I suspect the former.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> -- 
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110426/f9d2da39/attachment.html>