[gmx-users] no SOL in topology file after genbox command

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Fri Jun 29 11:35:24 CEST 2012

Hi everybody,
I wanted to add water in the box where I put the protein with the command

genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
2>>logErr 1>>logOut

The result is that I have indeed water (SOL) in the protein file
(3m71_water.gro). But there is a problem in the topology file (3m71.top).
Here I only have the line in the end after [ molecules ] where it is
written how many SOL were added to the structure:

SOL             14329

But in the [ moleculetype ] part of the topology file there is no SOL
mentioned. This causes an error when I want to call grompp.

SO my question is: why is there no SOL in the [ moleculetype ] part?

Best, Eva

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