[gmx-users] Character issues

[Kelsy Yuan]

Hi Justin and Mark,

Thank you very much for your helpful reply. There is not much information
given from the top part of terminal output, but I found the line is in the
[atom] section in mica1layer.itp file of my surface. This [atom] section is
edited manually, and it worked before in my previous calculations. So I'm
still having a hard time of what's going on. I have uploaded the involved
files here: https://drive.google.com/open?id=0BxefpKZ7B7yBQ1dVV3pqVUpON1k,
please take a look. I sincerely appreciate it.

Thanks again,
Kelsy

On 8 December 2016 at 12:00, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/8/16 2:43 PM, Kelsy Yuan 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
>> -------------------------------------------------------
>>
>>
> The input files that grompp reads are whatever you pass to it on the
> command line (.gro, .top, and .mdp) and the force field files.  Since this
> must be a custom force field, there are many potential places for problems,
> but something you created/edited must contain this line.  grompp doesn't do
> anything it's not told.
>
> If you need further help, you'll have to upload all of your files
> (everything listed above) to a file-sharing service and provide a link.
>
> Note that using -zero is potentially dangerous.  If your force field is
> missing interactions and you're just trying to get past them, that may
> generate an unstable system.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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>
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