Li, Yun wrote:
Hi,
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.
Mark
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