[gmx-users] Distance restraints

[Mark Abraham]

zhong qiang wrote:
> 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 ]

!! That's a bit like a car mechanic telling you your car won't start
because your battery is flat, and so you take it out and try again!

> 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?

Yep. The first step will be to spell it like it is in the manual...
"distance_restraints"

Mark