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

[Steven Neumann]

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?

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