[gmx-users] ions coupl to protein in .top

Yang Ye leafyoung81-group at yahoo.com
Wed Feb 7 11:23:42 CET 2007

Instead of correcting .top file, this error relates to index file. You
shall append the Ca ions to the SOL group for T-coupling.

# make_ndx -f your.gro
In the list printed, you shall see a SOL group and a Ca group adjacent
to each other.
Type "q" to quit and write the index file.

# vi index.ndx # or your favorite text editor
Find the Ca group by string "[ Ca ]", then remove the the line [ Ca ].

In your grompp command line, append an option -n

On 2/7/2007 5:09 PM, zhong qiang wrote:
> Hi :
> I have four calcium ions in .top file, But when I run grompp -f
> fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr
> The Error report:
> Fatal error:
> 4 atoms are not part of any of the T-Coupling groups
> I think there is not define bond about calcium ions in my .top file,
> How can I correct my top file?
> Could somebody tell me how to do ? Thank you very much
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