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
--
========================================
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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