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
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