[gmx-users] problem with specbonds

quantix1 at gmx.de quantix1 at gmx.de
Thu May 22 18:48:00 CEST 2003

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
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:
    ARG7     C64   0.140

Does it get confused because the C-terminus is defined interactively as

It is not a problem to add the bonds, angles etc. to the topology file once,
but I would have 
to do it many times, which is quite time consuming. Therefore, if you have
any suggestions,
I'd be very grateful,


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