[gmx-users] problem with genbox
Mark.Abraham at anu.edu.au
Fri Dec 15 00:36:13 CET 2006
Li, Yun wrote:
> I was very excited to discover Gromacs and decided to learn by following
> a few tutorials I found online. However, I ran into a problem: After
> filling up the simulation box with SPC water using genbox, the program
> backed up the topology file into another file with its name flanked by
> #, and left me with an empty topology file.
Read carefully the output from genbox - I expect there's an error there
that you've missed.
> Without knowing what had
> happened I went ahead and ran grompp, which exited with a fatal error,
> saying the number of atoms in the topology file does not match that of
> the coordinate file. I tried to use the backed up topology file, or to
> generate a new topology file using pdb2gmx, but ended up with the same
> error message. Grompp thinks there is no atom in the topology files.
Well, of course it will, if the .top file is empty!
> Does anyone know what is going on? Also, water molecules don’t seem to
> appear in topology files. Does that matter?
They get pulled in with the #include mechanism.
The general structure of a .top file is a series of [ moleculetype ]
sections, followed by a [ system ] section that describes the system as
a set of the predefined molecules. For water, the [ moleculetype ]
sections are contained in an .itp file that gets included by cpp. Your
solute is in the .top file directly, in the usual case. Please read
Chapter 5 fof the manual or more info.
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