[gmx-users] Character issues

[Mark Abraham]

Hi,

Which of your files has that line, and why is it so long? You aren't
sharing useful things like your command line and the terminal output, so
it's hard to say anything useful.

Mark

On Fri, 9 Dec 2016 05:52 Kelsy Yuan <kelsy.yuan at gmail.com> wrote:

> Hi Mark,
>
> Thanks for your quick reply. I tried to use Gromacs 5.0.6 to grompp, it did
> give me a little bit more information about the error, without mentioning
> "20s". However, I cannot find the exact position since I don't have that
> line in my input file. There is not much information about it on the
> website nor manual. I wonder is it possible to get some further
> explanations? Thank you in advance.
>
> -------------------------------------------------------
> Program grompp, VERSION 5.0.6
> Source code file:
> /usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112
>
> Fatal error:
> An input file contains a line longer than 4095 characters, while the buffer
> passed to fgets2 has size 4095. The line starts with: '1     AL1     1
>   UNL     A2'      ay1
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> Sincerely,
> Kelsy
>
> On 2 December 2016 at 14:52, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > What makes you think "_" is more relevant than "20s"?
> >
> > You could well have a better experience if you were not using a version
> of
> > software that is five years old.
> >
> > Matk
> >
> > On Fri, 2 Dec 2016 22:45 Kelsy Yuan <kelsy.yuan at gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I am trying to do an energy minimization of my system that contains
> > stearic
> > > acid molecules and an ionic surface. Every time I grompp I get the
> > > following error massage:
> > >
> > > Program grompp_s_mpi, VERSION 4.5.5
> > > Source code file: string2.c, line: 105
> > >
> > > Fatal error:
> > > An input file contains a line longer than 4095 characters, while the
> > buffer
> > > passed to fgets2 has size 4095. The line starts with: '20s'
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > >
> > > I checked every single input file as well as the force filed directory,
> > > none of them contains "_" when I viewed them on different text
> editors. I
> > > wonder does anyone know another solution or possible reasons for this
> > > issue?
> > >
> > > Thank you in advance,
> > > Kelsy
> > > --
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