I usually avoid this issue using "iso" e.g.:
solvatebox my_protein TIP3PBOX 12.0 iso
This way you get a cubic box with at least 12.0 A padding in each direction.
Hope this helps,
Cianna
On Fri, Sep 22, 2023 at 6:31 AM Carlos Simmerling via AMBER <
amber.ambermd.org> wrote:
> try solvateoct
>
> On Fri, Sep 22, 2023 at 9:28 AM Midhun K Madhu 1620103 via AMBER <
> amber.ambermd.org> wrote:
>
> > Hello all,
> >
> > This is somewhat a basic question: in any protein simulation, when using
> a
> > solvate box with a certain cutoff, such as 12 angstroms, tleap adds water
> > padding of 12 angstroms in all directions. However, the box generated
> will
> > be a cuboid. During simulation, the protein can rotate and align
> > perpendicularly to its starting orientation. If the protein is somewhat
> > like a stretched ellipsoid shaped rather than round or globe-like, this
> > rotation could destroy the 12 angstrom padding (in other dimensions) that
> > we used for the construction of the cuboid. Also, during simulation,
> there
> > is a chance that the rotation can make the protein interact with its own
> > image in smaller dimension axes. In that case, why is the cuboid box
> > required as an option to generate periodic boxes?
> >
> > with regards,
> >
> > --
> >
> > *MIDHUN K MADHU*
> > Ph.D Student
> > Dept. of Biological Sciences
> > IISER Bhopal
> > _______________________________________________
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> > AMBER.ambermd.org
> >
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Received on Fri Sep 22 2023 - 11:30:02 PDT
