AMBER Archive (2003)

Subject: saveAmberParm problems in xleap

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Tue May 06 2003 - 03:14:58 CDT


Dear Amber users,

I am trying to run a 20000 atom simulation (protein in
explicit water w/ PBC). However, whenever I set up the protein
+ water complex, xleap dies when it tries to create the
*.crd file.

> saveAmberParm prtn_wtBox prtn_wtBox.top prtn_wtBox.crd
.....*** He's dead Jim ***.....

It must be an array dimension problem in the initial
configuration of the program, but how can I enlarge the
array?

I noticed that someone posted a similar problem last year in the
amber reflector,

http://structbio.vanderbilt.edu/archives/amber-archive/2002/0489.phtml

However, there was no answer to this post. That post did provide a
"work around" (i.e., use tleap), but has this problem been solved?
What configuration files should I fix if so?

I gather from
http://structbio.vanderbilt.edu/archives/amber-archive/2003/0685.phtml
and some other posts that I can (at least in principle) do
calculations of this size.

Thank you.
Wayne