[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1

[Collins Nganou]

Dear Users,

 I am unable to generate the file.gro with  gromacs.4.6.3-1.
However, I have obtained the file.top after using

pdb2gmx -f TTb.pdb -o TT.gro -p TT.top -ignh
...

This appears after I have change the version of gromacs from 4.5-4 to
4.6.3-1
I am not able to find any error in the output.

I will be very grateful the receive any suggestion...

I wish you all a blessing weekend


Collins


My out put :

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 4 residues with 37 atoms

  chain  #res #atoms
  1 ' '     2     37

All occupancies are one
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
Processing chain 1 (37 atoms, 2 residues)
Identified residue DT3 as a starting terminus.
Identified residue DT4 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 2 residues with 63 atoms
Making bonds...
Number of bonds was 66, now 66
Generating angles, dihedrals and pairs...
Instruction non permise (core dumped)