AMBER Archive (2003)

Subject: Re: saveAmberParm problems in xleap

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Tue May 06 2003 - 08:42:13 CDT

Hi,
    I've used xleap to create solvated system that is as large as 70,000 atoms
and didn't have any crashes with either amber6 or amber7. Could it be
machine-specific? I have a dual PIII 800/Linux.

On Tuesday 06 May 2003 04:14, Wayne Dawson wrote:
> 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 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790