[gmx-users] error in grompp

[Justin A. Lemkul]

Serena Leone wrote:
> Hi all
> 
> I am trying to model a sulfated octasaccharide. I retrieved the topology 
> files from prodrg and I fixed them. The same procedure on a the 
> monosaccharide unit of the oligosaccharide I'm going to run worked 
> smoothly. After solvating the molecule, I try to pre-process it and I 
> obtain the following error:
> 
> -- Generated 279 of the 1225 non-bonded parameter combinations
> WARNING 1 [file "GI.top", line 993]:
>  Too few parameters on line (source file toppush.c, line 1168)
> processing coordinates...
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 469
> 
> Fatal error:
> number of coordinates in coordinate file (GI_wb.gro, 17431)
>             does not match topology (GI.top, 0)
> 
> 
> According to the wiki, the fact that no atom is recognized in the top 
> points to an incorrect location of the path for the cpp in the mdp, but 
> this is not the case (i double checked, plus this is exactly the same 
> mdp file that i used for other runs and that worked fine...). I also 
> checked for mispellings of atoms and residues names in the top, but 
> everything apparently fits. Do you have any idea of what else may cause 
> this behavior?

One can only blame cpp if the error messages show up as they appear on the wiki, 
but the output you've shown does not indicate that as a problem.  If this is not 
the case, there are several other possibilities.  Usually it's something simple, 
like a type in an #include line, or including the relevant .itp files in the 
wrong order, or something else less obvious.

It looks like there is another problem: "Too few parameters on line..." so I 
would explore that error to see if that is causing some failure in the grompp 
process.

-Justin

> 
> Thanks a lot
> Cheers,
> Serena
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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