[gmx-users] gmx error

[Rana Rehan Khalid]

Hi everybody

I am facing this error kindly guide me

hecking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 324 residues with 5193 atoms
Chain time...
Making bonds...
Number of bonds was 5261, now 5260
Generating angles, dihedrals and pairs...
Before cleaning: 13851 pairs
Before cleaning: 14001 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 14001 dihedrals, 1053 impropers, 9524 angles
          13737 pairs,     5260 bonds and     0 virtual sites
Total mass 36926.509 a.m.u.
Total charge -1.000 e
Writing topology
Processing chain 2 'B' (316 atoms, 39 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 71 donors and 55 acceptors were found.
There are 79 hydrogen bonds
Will use HISE for residue 7
Will use HISE for residue 29
Identified residue LEU1 as a starting terminus.
Identified residue THR39 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    HIS7
                   NE252
   HIS29  NE2226   1.978
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 39 residues with 633 atoms
Chain time...
Making bonds...
Number of bonds was 643, now 642
Generating angles, dihedrals and pairs...
Before cleaning: 1677 pairs
Before cleaning: 1707 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 1707 dihedrals,  137 impropers, 1154 angles
          1665 pairs,      642 bonds and     0 virtual sites
Total mass 4473.138 a.m.u.
Total charge 4.000 e
Writing topology
Including chain 1 in system: 5193 atoms 324 residues
Including chain 2 in system: 633 atoms 39 residues
Now there are 5826 atoms and 363 residues
Total mass in system 41399.647 a.m.u.
Total charge in system 3.000

regards