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

[Justin A. Lemkul]

Jose Borreguero wrote:
> 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:
> 

Using the -p flag will make all the necessary changes automatically.

> [ 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+
> 

Assuming you're using a new version of Gromacs (4.5.x), the naming scheme has 
changed.  Check the ions.itp for the force field you've chosen to use to set 
proper names.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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