[gmx-users] Error while using the CHARMM forcefield for NAD ligand in Gromacs

[BIJENDRA KHADKA]

Hello Everyone,
Recieved an following error while using the CHARMM forcefield for
NAD-protein interaction.
All suitable gromacs topology files for ligand was generated using the the
python script (and procedure) described in the MacKerell website.

The nad.itp file is attached herewith

Any suggestions would be greatly appreciated.


Step: Addition of ion.
Follwining is the error output:

NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 3260613728
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
ERROR 1 [file nad.itp, line 91]:
  No default Bond types
ERROR 2 [file nad.itp, line 104]:
  No default Bond types
ERROR 3 [file nad.itp, line 350]:
  No default U-B types
ERROR 4 [file nad.itp, line 352]:
  No default U-B types
ERROR 5 [file nad.itp, line 354]:
  No default U-B types
ERROR 6 [file nad.itp, line 450]:
  No default U-B types
ERROR 7 [file nad.itp, line 458]:
  No default U-B types
ERROR 8 [file nad.itp, line 459]:
  No default U-B types
ERROR 9 [file nad.itp, line 485]:
  No default Proper Dih. types
ERROR 10 [file nad.itp, line 486]:
  No default Proper Dih. types
ERROR 11 [file nad.itp, line 487]:
  No default Proper Dih. types
ERROR 12 [file nad.itp, line 489]:
  No default Proper Dih. types
ERROR 13 [file nad.itp, line 653]:
  No default Proper Dih. types
ERROR 14 [file nad.itp, line 654]:
  No default Proper Dih. types
ERROR 15 [file nad.itp, line 655]:
  No default Proper Dih. types
Excluding 3 bonded neighbours molecule type 'Protein_chain_R'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'NAD'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...

NOTE 2 [file topol.top, line 44763]:
  System has non-zero total charge: -10.999996
  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.


Regards,
Bijen
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