AMBER Archive (2002)

Subject: periodic box

From: Jiyoung Heo (jyheo_at_wag.caltech.edu)
Date: Fri Jul 26 2002 - 17:00:28 CDT

Dear all,

I am trying to do simulation with DNA dodecamer crystal structure. I
want to use the periodic box which is given in the pdb file of this
crystal. The problem is that the bounding box size of the model in one
direction is larger than the size of the crystal cell.

dimensions of the model: 32.763400 33.814293 49.569000
(I have got from 'setbox my_model' command)

dimensions of crystal cell: 25.300 41.700 66.000

I tried the 'setbox' command with specified buff values. Of course, in
the x direction, the buffer value is negative.
However, the box size did not change and it is still 32.763400 x
33.814293 x 49.569000.

Is there any way to change the size of the box as what I want?
Some program I am using recognizes the 'CRYST1' line in the pdb file and
builds a crystal cell automatically. Does the amber have this option?
Maybe not...

Thanks.

Jiyoung