which version of amber are you using? Amber7 has no
problems with "only" 20000 atoms. Actually, Amber6
shouldn't either.
On Tue, 6 May 2003, 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://amber.ch.ic.ac.uk/archive/200205/0098.html
>
> 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://amber.ch.ic.ac.uk/archive//all/4994.html
> and some other posts that I can (at least in principle) do
> calculations of this size.
>
> Thank you.
> Wayne
>
--
----------------------------------------------------------------------------
NOTE NEW MAILING ADDRESS & FAX NUMBER:
James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-514-3866
UCSF Box 2240 (email) caldwell.heimdal.ucsf.edu
600 16th Street
University of California
San Francisco, CA 94143-2240
----------------------------------------------------------------------------
Received on Tue May 06 2003 - 14:53:01 PDT
