From jingxing at vt.edu  Tue Jul 15 07:31:15 2008
From: jingxing at vt.edu (jingxing at vt.edu)
Date: Tue, 15 Jul 2008 10:31:15 -0400
Subject: [Dockdev] docking:protein-DNA
Message-ID: <1216132275.487cb4b32b74c@webmail.vt.edu>

Hello,

   I am trying to dock protein with DNA (ligand). But the DNA is too big, with
about 700 atoms.
   When I ran it, it tells me memory exhausted.
   Is there anyone who knows what I can do?
   Thank you very much.

Jing
Bio
Virginia Tech


From xubeisi at gmail.com  Tue Jul 15 08:14:46 2008
From: xubeisi at gmail.com (Beisi Xu)
Date: Tue, 15 Jul 2008 10:14:46 -0500
Subject: [Dockdev] docking:protein-DNA
In-Reply-To: <1216132275.487cb4b32b74c@webmail.vt.edu>
References: <1216132275.487cb4b32b74c@webmail.vt.edu>
Message-ID: <7d58a3b00807150814x12552943lee647540369e8604@mail.gmail.com>

700 atoms is not that much...
try dynamics arrays like vector in C++

On Tue, Jul 15, 2008 at 9:31 AM,  <jingxing at vt.edu> wrote:
> Hello,
>
>   I am trying to dock protein with DNA (ligand). But the DNA is too big, with
> about 700 atoms.
>   When I ran it, it tells me memory exhausted.
>   Is there anyone who knows what I can do?
>   Thank you very much.
>
> Jing
> Bio
> Virginia Tech
>
> _______________________________________________
> Dockdev mailing list
> Dockdev at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dockdev
>



-- 
Beisi Xu, Ph.D Candidate
PSE at USTC
Zhou at CCBB@IUPUI
Phone:	+1-814-441-6038
MSN:	xubeisi at hotmail.com
http://picasaweb.google.com/xubeisi/100CANON/photo#5152479988430216194