I faced this problem and the best solution is to install amber on a large
supercomputer cluster.Entropy calculation requires a huge memory based on
bio molecule atom numbers.
-----Sushil Mishra [1]<sushilbioinfo.gmail.com> wrote: -----
To: AMBER Mailing List [2]<amber.ambermd.org>
From: Sushil Mishra [3]<sushilbioinfo.gmail.com>
Date: 03/21/2011 12:15PM
Subject: Re: [AMBER] nmode memory issue
There is an article by Ulf Ryde et al, in JCAMD, Volume 23, Number 2,
63-71,
DOI: 10.1007/s10822-008-9238-z
I think this could give you better understanding on using nmode on same
trajectory but by truncating the system.
hope it helps
/Sushil
On Mon, Mar 21, 2011 at 6:01 PM, amit dong [4]<dongamit123.gmail.com>
wrote:
> Hello,
>
> I am doing entropy calculations on a protein-ligand complex using nmode
in
> Amber11. I have MD done on a dimer complexed with ligand. My system has
> ~9500 atoms and I don't have enough memory to do the calculations. The
> system crashes with an error (FATAL: allocation failure in vector() ).
>
> I am planning to strip off one of the monomer. Is there any quicker way
of
> doing it without having to redo the MD with the monomer.
>
> Thanks
> Amit
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> [6]http://lists.ambermd.org/mailman/listinfo/amber
>
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References
1. mailto:sushilbioinfo.gmail.com
2. mailto:amber.ambermd.org
3. mailto:sushilbioinfo.gmail.com
4. mailto:dongamit123.gmail.com
5. mailto:AMBER.ambermd.org
6.
http://lists.ambermd.org/mailman/listinfo/amber
7. mailto:AMBER.ambermd.org
8.
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Mar 21 2011 - 11:00:03 PDT
