AMBER Archive (2000)
Subject: leap problem about periodic boundary box
From: K. Watanabe. (watanabe-katsuhiro_at_hitachi-ul.co.jp)
Date: Wed Sep 27 2000 - 21:54:02 CDT
Dear AMBER users
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.].
1. Does anyone have any knowledge to solve this problem
of settin periodic boundary box size?
2. If I can solve this problem, does xLeap output
TOP & CRD files over 999,999 atoms ?
thanks in advance
Hitachi ULSI Systems Ltd.