AMBER Archive (2002)

Subject: Re: periodic box

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Sat Jul 27 2002 - 09:41:50 CDT

Jiyoung

Maybe the solution is to just delete all the waters and then add them
back unless there is some particular reason to do otherwise.

Pete Gannett

>>> Jiyoung Heo <jyheo_at_wag.caltech.edu> 07/26/02 06:00PM >>>
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