[gmx-users] big protein dynamics with gromacs 3.2.1

Adriana Pietropaolo adriana at ms.fci.unibo.it
Tue Nov 29 17:54:50 CET 2005

On Tue, 29 Nov 2005, Tsjerk Wassenaar wrote:

> Hi Adriana,
> pdb2gmx should be able to detect SS bonds automatically, though in some
> cases fails to do so (if the distance is too large). If you know that you're
> missing a SS bond you can add an entry to the file specbond.dat in the
> directory $GMXDIR/share/top (maybe first copy the file to your directory).
> Copy the line referring to the cys-bridge and change the distance to the
> distance in your structure. Running through pdb2gmx should then fix your
> problem.
> With regards to the other issue, neither editconf nor genbox changes your
> structure (there's no cutting). There may be shifts over the periodic
> boundaries, but these don't affect the resulting simulation system.
> Cheers,
> Tsjerk
Thanks a lot,
I would like to ask you if there is a flag (like pdb2gmx
-...) so that pdb2gmx can read in local specbond.dat, 
because I can't modify this file in the  root directory, 
so I copied this file in my home directory.
As regarding with the other question for a sample already with water 
molecules, why pdb2gmx generates a topology with 3 solvent group like SOL 
SOL SOL? the water molecules are 29915 and the pdb generated from MD 
simulation is divided in layers and not uniformly solvated...
 Thanks in advance,

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