Interesting that you have your Ca2+ ions in the beginning of your
structure file. In this case, remove the line [ SOL ] and replace [ CA ]
with [ SOL ].
Although, changing your mdp file to have "Protein Non-Protein" is simpler.
The rationale behind is that the *groups* included for the tc-grps shall
cover all atoms.
On 2/7/2007 9:34 PM, 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:
grompp -n index.ndx -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o
fullmd.tpr
But Error still there.
Could somebody tell me how to do?
Thank you very much!
------------------------------
Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education
College of Animal Sciences and Technology
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China
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