[gmx-users] Understanding comments in pdb2gmx output

[Agnivo Gosai]

Dear Gromacs Users

I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO )
. I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported
into it. I had cleaned the PDB file off crystal waters and a small chemical
ligand ( which I dont require ) before passing it through pdb2gmx.

The topology has been successfully generated.

However I am concerned with the following comments in the output of pdb2gmx
, I am copy pasting 3 blocks from the output :-

#############################
There are 3 chains and 0 blocks of water and 247 residues with 2590 atoms

  chain  #res #atoms
  1 'D'    15    315
  2 'L'    27    222
  3 'H'   253   2053

WARNING: there were 0 atoms with zero occupancy and 9 atoms with
         occupancy unequal to one (out of 2590 atoms). Check your pdb file.
#################################
Processing chain 3 'H' (2053 atoms, 253 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 395 donors and 366 acceptors were found.
There are 535 hydrogen bonds
Will use HISE for residue 57
Will use HISE for residue 71
Will use HISE for residue 91
Will use HISE for residue 119
Will use HISE for residue 230
Now there are 253 residues with 4078 atoms
############################################
Chain time...
Making bonds...
Warning: Long Bond (2429-2431 = 0.805851 nm)
Number of bonds was 4137, now 4136
##########################3

I would like to know the meaning of these messages. Also I am reading the
GROMACS manual for further info.

Best ,

Agnivo
Iowa State , USA