Error: Atom index out of bounds

[vijay singh]

I am setting up an implicit solvent simulation using amber force field.

When I want to do an energy minimization, I get an error -

Fatal error:
[ file spc.itp, line 37 ]:
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology section "bonds"
in a part belonging to a different molecule than you intended to.
In that case move the "bonds" section to the right molecule

I looked through various forums (on Gromacs too) for similar problems and solutions. There were suggestion of making changes to spc.itp file by incorporating lines like -

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 amber99_54 1 SOL OW 1 -0.82 15.99940
2 amber99_55 1 SOL HW1 1 0.41 1.00800
3 amber99_55 1 SOL HW2 1 0.41 1.00800


Should the spc.itp be invoked even if I have no explicit water in my simulations?

I saw no mention of such a problem on http://chemistry.csulb.edu/ffamber/.

Any suggestion on where I may be going wrong?

Thanks,
VJ

[vijay singh]

Update on this is that, I just commented out the section in *.top file that's looking for "spc.itp". With this, I continued with rest of the simulation and no errors appeared. The graphical output as seen in VMD appears normal.

I am not sure if doing this is legitimate? I am also still in dark about the reason for this error to occur and the right way to deal with it?