[gmx-users] problem with specbonds

[David]

On Thu, 2003-05-22 at 18:47, quantix1 at gmx.de wrote:
> Hi all,
> 
> I'am trying perform a cyclization using pdb2gmx, so I wouldn't have to edit
> the topology
> file by hand. I'd like to connect the side chain of ornithine to the
> C-terminus of the last
> amino acid. The line I have added to specbonds.dat looks like this:
> 
> ORN     NE      1       ARG     C       1       0.2     ORN     ARG
                                                  ~~~
  change this to                                 0.14

> It's recognized by pdb2gmx,but the ring closure is not made.
> 
> Opening library file specbond.dat
> 6 out of 6 lines of specbond.dat converted succesfully
> Special Atom Distance matrix:
>                     ORN3
>                     NE20
>     ARG7     C64   0.140
> 
> Does it get confused because the C-terminus is defined interactively as
> well?
> 
See above. Report further problems back to the list.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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