AMBER Archive (2000)

Subject: Re: leap problem about periodic boundary box

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Sep 27 2000 - 22:54:04 CDT

         Recently, we want to do very large size protein MD
        by using sander5.0, and we are in difficulties for making
        TOP & CRD files in xLeap in AMBER 5.0.
         When I edited protein files in xLeap, I needed to set
        [90Ang. * 90Ang. * 130Ang.] size of periodic boundary box,
        but I can't do it. xLeap recognized
        not [90Ang. * 90Ang. * 130Ang.]
        but [90Ang. * 90Ang. * 30Ang.].

        Question
        1. Does anyone have any knowledge to solve this problem
          of settin periodic boundary box size?

The format of setbox would be

> setbox DG { 90 90 130 }
Box dimensions: 187.446419 192.339006 272.066221

but as you can see, the numbers refer to the clearance between
the molecule and the side of the box, in both directions along
each axis. Perhaps you can make this work for you. Also, alignaxes
may be used first, if desired. Note that v6 leap can be obtained at
ftp://odin.compchem.ucsf.edu/pub/a6.tar.gz

        2. If I can solve this problem, does xLeap output
          TOP & CRD files over 999,999 atoms ?

It might, but I suspect that they would be worthless owing to
the format limitations, i.e. sander would read garbage since it
expects fixed formats of I6. I believe this limitation may be
under discussion by the developers.

Bill Ross