[gmx-users] Error while using the CHARMM forcefield for NAD ligand in Gromacs-3

[BIJENDRA KHADKA]

 Dear Justin,
As per your suggestion on my previous email, I tried using the ligand (NAD)
input files generated using CHARMM-GUI (files are attached herewith).
However, I received the following error.

(previous email:Message-ID: <d3e21a78-9b0c-88fa-a6d7-c60c56a0e488 at vt.edu>)

Any suggestion regarding this matter would be greatly appreciated.

command: ./gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
ERROR:
ARNING 15 [file nad.prm, line 21]:
  Too few parameters on line (source file
  /usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)


WARNING 16 [file nad.prm, line 22]:
  Too few parameters on line (source file
  /usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)


WARNING 17 [file nad.prm, line 23]:
  Too few parameters on line (source file
  /usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)


WARNING 18 [file nad.prm, line 25]:
  Too few parameters on line (source file
  /usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)


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 4 [file NAD.itp, line 95]:
  No default Bond types


ERROR 5 [file NAD.itp, line 96]:
  No default Bond types


ERROR 6 [file NAD.itp, line 118]:
  No default Bond types


ERROR 7 [file NAD.itp, line 357]:
  No default U-B types


ERROR 8 [file NAD.itp, line 358]:
  No default U-B types


ERROR 9 [file NAD.itp, line 359]:
  No default U-B types

ERROR 22 [file NAD.itp, line 494]:
  No default Proper Dih. types


ERROR 23 [file NAD.itp, line 495]:
  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: -9.999996
  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.
-------------------------------------------------------
Program gmx grompp, VERSION 5.1.4
Source code file:
/usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 605

Fatal error:
number of coordinates in coordinate file (solv.gro, 46287)
             does not match topology (topol.top, 46288)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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