[gmx-users] Re: Distance restraints

[zhong qiang]

Message: 2
>Date: Wed, 07 Feb 2007 11:12:34 +1100
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] Distance restraints
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <45C91972.6060208 at anu.edu.au>
>Content-Type: text/plain; charset=GB2312
>
>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
>

Thank you very much! The problem has been solved by your advice!

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