Qiang Zhong wrote:
Hollow:
I have post my question last time,my emailbox can not work, So I post
again.
I have 4 calcium ions bind at protein, when I use command:
grompp -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr
I got error message:
Fatal error:
4 atoms are not part of any of the T-Coupling groups
I got a advice to use :
make_ndx -f minimized_water.gro
Then I got a file index.ndx
I find the line in index.ndx ,just like below:
57378 57379 57380 57381
[ CA ]
1 2 3 4
[ SOL ]
Then I delete them,and run again:
That wasn't the advice Yang Ye gave you... see
http://www.gromacs.org/pipermail/gmx-users/2007-February/025792.html
For a simpler solution, see
http://www.gromacs.org/pipermail/gmx-users/2007-February/025796.html
Mark
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