AMBER Archive (2005)

Subject: Re: AMBER: carnal problem

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Sep 08 2005 - 10:51:34 CDT

> I am using carnal to analyse H-bonds including solvent molecules. The size
> of the molecule is 928 residues and there are around 27000 water
> molecules. While running the carnal, I get the following error:
>
> "malloc 1480614768 bytes: Cannot allocate memory
> Not enough memory: try 'limit' to see
> if e.g. 'unlimit datasize' may help.
> Otherwise, increasing swap space may
> be possible"
>
> I have tried increasing swap space from 1GB to 2GB, but I get the same
> error. I would appreciate any kind of help.

Did you try 'limit' etc. first? Swap is probably irrelevant if
limits are holding you back.

It may be that you are simply trying to do too much for your
operating system. Seeing your input file and knowing what
sort of machine you are on might help.

Carnal will be dropped from Amber due to lack of interest in
supporting it, so you could also consider trying ptraj.

Bill
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu