Hi:
I want to constuct my .top file, In my molecular system four calcium
ions binding at four site, I use pdb2gmx make a top file, But there is not
topology information about calcium ions, I insert a distance restraints in
.top file, just like below:
[ distance restraints ]
; ai aj type index type’ low up1 up2 fac
1460 207 1 2 1 0.0 0.3 0.4 1.0
1460 208 1 2 1 0.0 0.3 0.4 1.0
1460 210 1 2 1 0.0 0.3 0.4 1.0
1460 229 1 2 1 0.0 0.3 0.4 1.0
.........................
then I run
grompp -f fullmd_sol.mdp -c minimized_water.gro -p 1ckk.top -o fullmd.tpr
But error message present:
ERROR 1 [file "1ckk.top", line 9029]:
Invalid directive distance restraints
Then I delete line [ distance restraints ]
the error report:
Fatal error:
Incorrect number of parameters - found 4, expected 3 or 6.
Could somebody tell me how to add a distance restraints correctly?
Thank you very much!
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