[gmx-users] Character issues

[Justin Lemkul]

On 12/10/16 6:21 PM, Kelsy Yuan wrote:
> 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.
>

The entire [atoms] section shows up as a single line, interspersed with ^M, 
which are malformed line endings.

Make sure you're using a plain text editor to do anything, and if you're on 
Windows, use dos2unix as needed (and preferably, a proper editor).

-Justin

> 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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-- 
==================================================

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

==================================================