[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

[Paul Buscemi]

Run with a maxwarn 1. If it runs then there is a deeper problem. If does not go it's probably a typo. Bet it's the latter

PB

> On Aug 1, 2019, at 2:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> 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