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

[Justin Lemkul]

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

-- 
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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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