[gmx-users] Newbie: How to modify the topology file after adding ions?

[Jose Borreguero]

Dear Gromacs users,

Im new to gromacs and I'm following a tutorial (
http://nmr.chem.uu.nl/~tsjerk/course/molmod/). Unfortunately, the tutorials
doesn't say anything about how to update the topology file after using
'genion' to replace a few water molecules with ions.
I manually edited the topology file and updated the number of water
molecules and added the number of ions:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
SOL              7791
Na+              26
Cl-              23

But then when I tried to preprocess the structure with grompp, I got an
error:

Fatal error:
No such moleculetype Na+

Any help will be greatly appreciated!

Jose M. Borreguero
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