[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Justin Lemkul]

On 8/1/19 3:50 PM, Mohammed I Sorour wrote:
> Dear Gromacs users,
>
> I'm running MD simulation on a couple of DNA systems that only vary in
> sequence. Most of the runs worked just fine, but surprisingly I have one
> system that I got an error in the NVT equilibration step.
> I'm following the
> tutorialhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
>
> rogram:     gmx mdrun, version 2016.3
> Source file: src/gromacs/options/options.cpp (line 258)
> Function:    void gmx::Options::finish()
>
> Error in user input:
> Invalid input values
>    In option s
>      Required option was not provided, and the default file 'topol' does not
>      exist or is not accessible.
>      The following extensions were tried to complete the file name:
>        .tpr
>
> I'm pretty sure that I have the .tpr  files in the local directory. I have
> read the previous reviews of the Gromacs mailing list, and I know that
> it would be a problem with the toplogy file. The toplogy files looks
> so far good to me.

There's a typo in your command or the input file you think is there is 
not. You didn't provide your mdrun command (please always do this) but I 
suspect the former. If mdrun does not find the file you specify, it 
looks for the default file name, which is topol.tpr. That's also not 
there, so you get a fatal error.

> Here is the only thing I can susbect, but I don't know if this is the
> cause, but also I'm still wondering why: So When I generated my ssytem
> topology using pdb2gmx
>
>
> "Now there are 3969 atoms and 124 residues
> Total mass in system 37825.764 a.m.u.
> Total charge in system -118.000 e"
>
> But when I start the solvation, the total charge of the system changes
> and is no more an intger:
>
> "NOTE 2 [file topol.top, line 51]:
>    System has non-zero total charge: -117.999968
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer."
>  From the gromacs documentations, it's fine to have that slight
> non-integer charge, but I'm wondering why is that happening?!

You have a large system with a lot of charges. You're going to 
accumulate rounding error. This is not a problem.

-Justin

> I ran the energy minimization using these files, and it worked well,
> it only failing with the NVT step.
>
> I deeply aplogize for the lenghty email and for submitting the same
> email previously. The first one was not complete and was sent by
> mistake.
>
> Sincerely,
>
> Mohammed Sorour

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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