[gmx-users] how to create a .top file from a .gro?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 7 00:51:43 CET 2007

Aline wrote:
> Hi list,
> I want to create a .top form an already run dinamics, using the .gro
> result from the last trajetory frame. I already used the pdb2gmx, but
> when i run the grompp, using the already cited .gro and new .top, i
> receive the error that my .gro and .top doesnt have the same number of
> atoms.
> is there something im missing?

Have a look at the very bottom section of your .top file. I expect you 
will see there that you have only your solute, and not your solvent, or 
your ions, which were added to the .top after pdb2gmx was used. You need 
to reproduce the whole of your setup protocol, not just the first step. 
Better still, don't discard your old topology!


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