[gmx-users] problem with genbox

[Mark Abraham]

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