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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Received on Fri Sep 22 2023 - 07:00:02 PDT
