if you want your trajrctory with the protein in center you can use some
residues to define a center and then image back everything using ptraj.
ptraj input file>
trajin your-trajrctory-file
trajout another-trajrctory-file filetype box
center :a-b (a to b are numbers of residus to consider in center of
geometry)
image
go
use this input file as
ptraj your-topology-file ptraj-input-file
On Sat, Jun 23, 2012 at 11:04 AM, Adam Jion <adamjion.yahoo.com> wrote:
> Hi,
> How does restraining a residue work in Amber?
> For example, if I have a giant protein that traverse across a wall of a
> simulation box under periodic boundary conditions, and if I were to
> restrain the protein to these initial coordinates, will the simulation box
> be able equilibrate under NPT simulation?
>
> Regards,
> Adam
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>
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Received on Sat Jun 23 2012 - 03:00:02 PDT
