[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

[Mohammed I Sorour]

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.

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?!

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