[gmx-users] line longer than 4095 characters - help
s.neumann08 at gmail.com
Fri Nov 9 11:27:23 CET 2012
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
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
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
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 :(
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