[gmx-users] grompp error- Excluding 3 bonded neighbours-Fatal error

[Mark Abraham]

Dean Cuebas wrote:
> Dear users,
> I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
> 
> I¹ve tried to get grompp to work, but I keep getting the following message:
> _______________________________________________________
> 
>>> creating statusfile for 1 node...
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>>> checking input for internal consistency...
>>> calling /usr/bin/cpp...
>>> processing topology...
>>> Generated 165 of the 1596 non-bonded parameter combinations
>>> Excluding 3 bonded neighbours for Protein             1
>>> Excluding 3 bonded neighbours for IN4                 1
>>> Excluding 2 bonded neighbours for SOL              8756
>>> NOTE:
>>>   System has non-zero total charge: 7.999998e+00
>>>
>>> processing coordinates...
>>>
>>> -------------------------------------------------------
>>> Program grompp, VERSION 3.3.2
>>> Source code file: grompp.c, line: 448
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (trp_b4ion.pdb, 28394)
>>>              does not match topology (trp.top, 28402)
>>> -------------------------------------------------------
>>>
> It appears because grompp is ³excluding² the bonded neighbors is what¹s
> making me end up with the different number of coordinates in my coordinate
> and topology files.

No, "exclusions" are something else related to the structure of the 
force field - atoms connected by bonds shouldn't also be modeled with 
non-bonded interactions. The coincidence of 28402-28394=8 equaling 3+3+2 
is just that.

Rather more significant is that you have a non-zero charge of (rounded) 
8 and you seem to be part way through a process of replacing water 
molecules with ions, which usually leaves a system neutral. I'd guess 
you've done something wrong there - most likely mislabeled a file.

Mark