[gmx-users] Character issues

Thu Dec 8 21:00:13 CET 2016

Hi,

That's the end of the terminal output. What came before it is a clue.

Mark

On Fri, 9 Dec 2016 06:44 Kelsy Yuan <kelsy.yuan at gmail.com> wrote:

> Hi Mark,
>
> Sorry for the confusion. The command I use is: grompp -p topol.top -f
> engmin.mdp -c 16+mica.gro -zero, I want to do the energy minimization for
> my system that contains 16 stearic acid and a mica surface. I checked all
> my input files as well as the force field files, there is no such line.
> Following is the terminal output:
> -------------------------------------------------------
> 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
> -------------------------------------------------------
>
> Thanks for trying to help,
> Kelsy
>
> On 8 December 2016 at 11:06, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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