[gmx-users] Protein-ligand complex energy minimization

[Indu Kumari]

Grompp terminated and shows following warning and notes:
NOTE 1 [file topol.top, line 57]:
  System has non-zero total charge: -0.675997
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Warning: atom name 3706 in topol.top and fws_ion.pdb does not match (O1 -
OW)
Warning: atom name 3707 in topol.top and fws_ion.pdb does not match (P1 -
HW1)
Warning: atom name 3708 in topol.top and fws_ion.pdb does not match (O2 -
HW2)
Warning: atom name 3709 in topol.top and fws_ion.pdb does not match (O3 -
OW)
Warning: atom name 3710 in topol.top and fws_ion.pdb does not match (O -
HW1)
Warning: atom name 3711 in topol.top and fws_ion.pdb does not match (P2 -
HW2)
Warning: atom name 3712 in topol.top and fws_ion.pdb does not match (O5 -
OW)
Warning: atom name 3713 in topol.top and fws_ion.pdb does not match (O6 -
HW1)
Warning: atom name 3714 in topol.top and fws_ion.pdb does not match (O4 -
HW2)
Warning: atom name 3715 in topol.top and fws_ion.pdb does not match (NA -
OW)
Warning: atom name 3716 in topol.top and fws_ion.pdb does not match (NA -
HW1)
Warning: atom name 3717 in topol.top and fws_ion.pdb does not match (NA -
HW2)
Warning: atom name 3718 in topol.top and fws_ion.pdb does not match (NA -
OW)
Warning: atom name 3719 in topol.top and fws_ion.pdb does not match (NA -
HW1)
Warning: atom name 3720 in topol.top and fws_ion.pdb does not match (NA -
HW2)
Warning: atom name 3721 in topol.top and fws_ion.pdb does not match (NA -
OW)
Warning: atom name 3722 in topol.top and fws_ion.pdb does not match (NA -
HW1)
Warning: atom name 3723 in topol.top and fws_ion.pdb does not match (NA -
HW2)
Warning: atom name 3724 in topol.top and fws_ion.pdb does not match (NA -
OW)
Warning: atom name 3725 in topol.top and fws_ion.pdb does not match (NA -
HW1)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 57]:
  43 non-matching atom names
  atom names from topol.top will be used
  atom names from fws_ion.pdb will be ignored


Analysing residue names:
There are:   350    Protein residues
There are:     4      Other residues
There are:    15        Ion residues
There are: 21556      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 205188.00
Largest charge group radii for Van der Waals: 6.365, 3.730 nm
Largest charge group radii for Coulomb:       6.365, 4.811 nm

WARNING 2 [file em.mdp]:
  The sum of the two largest charge group radii (11.176151) is larger than
  rlist (1.000000)


Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.111 0.111 0.111
Estimate for the relative computational load of the PME mesh part: 0.29
This run will generate roughly 5 Mb of data

I am not able to solve this. Please help.
With regards,
Indu