AMBER Archive (2006)

Subject: Re: AMBER: nmode: number of atoms limitation

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Aug 30 2006 - 08:01:58 CDT

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_at_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
 
 Cell: +90-(536)-4813012
 
 E-Mail:cenk_andac_at_yahoo.com

                 
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