If your "protein" radius is set very high--such that it completely fills
the box--then AddToBox will be unable to add any molecules. In its
recursive attempts to add molecules, it is reducing the SOLVENT bump
radius, letting "solvent" molecules get packed more tightly together
(presumably, what you are adding is small and won't get tangled up in
itself too easily). The "protein" (or, however many atoms you define as
such) is treated as sacrosanct and AddToBox will not compromise -RP to
place molecules increasingly close to that part of your simulation.
AddToBox is expected to be followed by a trip through tleap and the energy
minimization, which should undo any clashes created by the solvent bump
radius reduction.
Dave
On Tue, May 2, 2017 at 9:24 PM, David Case <david.case.rutgers.edu> wrote:
> On Tue, May 02, 2017, sylvester kisembo wrote:
>
> > Has anyone had trouble recently getting AddtoBox to work in Ambertools
> 16/17?
> > I have tried this command on my machine and on the super computer:
> > AddToBox -c start.pdb -a input.pdb -na 7 -o combo.pdb -P 26 -RP 3.0 -RW
> > 6.0 -G 0.2 -V 1
>
> I use it all the time...from your output, it looks like the path for
> recursive calls may not be correct. Type "AddToBox" with no arguments to
> see the options. Make sure that your AMBERHOME variable is correctly set,
> and that AddToBox is actually in $AMBERHOME/bin.
>
> I'm not sure what is in "input.pdb", but assinging a relativel large radius
> of 6 Ang. might be a problem. Have you tried smaller radii?
>
> >
> > But i never get any molecules added even after recursive tries. This is
> always the result:
> > AddToBox >> Added 0 residues.
> > AddToBox >> Residue goal not achieved.
> > AddToBox >> Re-attempting with solvent clipping radius 4.3740.
> > GetPDB >> Found 26 atoms in combo.pdb.
> > GetPDB >> Bracketed 1 residues.
> >
> > GetPDB >> Found 26 atoms in L.pdb.
> > GetPDB >> Bracketed 1 residues
>
> Can you post the full output? You may need to provide the files and the
> actual command line you used. (Note that the program refers to "L.pdb",
> whereas the command line above has no such file.)
>
> ....thx...dac
>
>
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Received on Tue May 02 2017 - 20:00:02 PDT
