[gmx-users] line longer than 4095 characters - help

[Justin Lemkul]

On 11/9/12 7:40 AM, Steven Neumann wrote:
> On Fri, Nov 9, 2012 at 12:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 11/9/12 5:27 AM, Steven Neumann wrote:
>>>
>>> Dear Gmx Users,
>>>
>>> I used pdb2gmx to generate topology of the new molecule of which
>>> parameters I added to ffbonded.itp and aminoacids.rtp creating new
>>> resiude:
>>>
>>> pdb2gmx -f LIG.pdb -o LIGproc.pdb -p topol.top
>>>
>>> Back Off! I just backed up topol.top to ./#topol.top.1#
>>> Processing chain 1 'X' (49 atoms, 3 residues)
>>> There are 0 donors and 0 acceptors
>>> There are 0 hydrogen bonds
>>> Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA.
>>> Warning: Starting residue LIG2 in chain not identified as Protein/RNA/DNA.
>>> Warning: Starting residue FE3 in chain not identified as Protein/RNA/DNA.
>>> Problem with chain definition, or missing terminal residues.
>>> This chain does not appear to contain a recognized chain molecule.
>>> If this is incorrect, you can edit residuetypes.dat to modify the
>>> behavior.
>>> 8 out of 8 lines of specbond.dat converted successfully
>>> Opening force field file ./charmm27mod.ff/aminoacids.arn
>>> Opening force field file ./charmm27mod.ff/dna.arn
>>> Opening force field file ./charmm27mod.ff/rna.arn
>>> Checking for duplicate atoms....
>>> Now there are 3 residues with 49 atoms
>>> Making bonds...
>>> Number of bonds was 46, now 46
>>> Generating angles, dihedrals and pairs...
>>> Before cleaning: 114 pairs
>>> Before cleaning: 114 dihedrals
>>> Keeping all generated dihedrals
>>> Making cmap torsions...There are  114 dihedrals,    2 impropers,   76
>>> angles
>>>              114 pairs,       46 bonds and     0 virtual sites
>>> Total mass 446.147 a.m.u.
>>> Total charge -0.000 e
>>> Writing topology
>>>
>>> Back Off! I just backed up posre.itp to ./#posre.itp.1#
>>>
>>> Writing coordinate file...
>>>
>>>
>>>
>>> Then when i try to process to grompp:
>>>
>>> grompp -f minim.mdp -c LIGp.pdb -p topol.top -o em.tpr
>>>
>>> An input file contains a line longer than 4095 characters, while the
>>> buffer passed to fgets2 has size 4095. The line starts with: '20s'
>>>
>>> I cannot get rid of this. When I process without topology of the new
>>> molecule (e.g. processing protein with pdb2gmx and then grompp)
>>> everything is fine. It is not the fault of gurgle.dat, installation of
>>> Gromacs (I tried on 3 machines) surely. I also checked lenght of lines
>>> in topol.top, everything is fine.
>>>
>>> Please, advise, I loose my time :(
>>>
>>
>> You probably have some unrecognized line break in one of the files.  Try
>> dos2unix.
>>
>> -Justin
>
> I do this every time after generatin each file. It does not help.
> Would you kindly try to process grompp using my files?
>

Send me the files off-list and I will have a look.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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