[gmx-users] INTRA-molecular disulphide bridges.

[K.A.Feenstra]

Leonardo Manzoni wrote:
> 
> Actually the situation is the following:
> I want to run two simulations of the  peptide, one with CYS-CYS
> intramolecular bond, and the other without it.
> Using the -ss option of pdb2gmx I always obtain the same topology, and the
> same output in both cases
> should I define (or delete) the bond by hand?

That should in principle work. However, since it doesn't try this:
pdb2gmx reads a file which specifies the extra bonds to generate.
For gromacs 3.0 this can be found at $GMXDATA/top/specbond.dat,
usually somewhere under /usr/local. You can make an empty version
of the file in your local directory, however it must contain a
count of the number of lines, which is then 0 (zero).
The command:
echo 0 > specbond.dat
should do the trick. Now pdb2gmx wil not make any extra bonds, and
thus no s-s bridge.

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
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|             | "Why, how now, Claudio ! Whence Comes this Restraint|
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