I do not know what system you currently use but
you might want to upgrade to a 64 bit system with lots of memory or perhaps
use a parallel computing facility in your area to take advantage of shared memory allocation. You may also need to increase maximum atom number ( find the line " parameter (maxatom=5600)" ) in $HOME/amber/src/nmode/sizes2.h
to your needs such as "maxatom=20000" and recompile nmode.
good luck.
jenk
AYTUG TUNCEL <ATUNCEL.ku.edu.tr> wrote: Dear Amber users,
I am trying to do nmode calculation of mm_pbsa method using amber8. My protein is dimeric composed of totally 13776 atoms (both chains have nearly equal length). I am wondering about the maximum number of atoms that nmode can be applied. As far as I found in the archive it is about 8000 atoms. If this is the case how can I apply the method to my system, is there any trick about changing a parameter? thanks in advance...
Aytug
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Cenk Andac, M.S., Ph.D. Student
School of Pharmacy at
Gazi University-Ankara Turkiye
Address: Bandirma Sok. No:6
Etiler, Ankara, 06330 Turkey
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E-Mail:cenk_andac.yahoo.com
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Received on Sun Sep 03 2006 - 06:07:03 PDT
