[gmx-users] topology and coordinate file not matching after grompp
cma1g09 at soton.ac.uk
Wed Jul 31 12:04:59 CEST 2013
I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.
Basically, I am trying to mix 2 different proteins in one box and after
doing my grompp to neutralise the system, I get the error number of
coordinates in coordinate file (solvated.gro, 85059) does not match topology
This is how my topology file looks:
;Include the force field
; Include chain topologies
;Include water topology
;Include generic ion topology
[ system ]
Two proteins in water
[ molecules ]
How can I deduce from this data that the number of coordinates in topol.top
is 85079. And what exactly should I do to reduce the number of molecules
here so that the 2 files have the same number of coordinates.
I will really appreciate the help. I am pretty new with MD simulations
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