AMBER Archive (2009)

Subject: Re: [AMBER] How to split mdcrd files

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Sun Nov 15 2009 - 15:06:34 CST


> I am trying to do hydrogen bond analysis for my protein dna complex, but the
> problem is that my system is very big and my simulation is also of 20 ns.
> That is why ptraj is giving segmentation error, i think because my mdcrd

The ptraj output file should show estimates of memory required. I
personally would break up the h-bond analysis into multiple smaller runs
by putting a short list of donors in each along with the full acceptor
list...

--tec3

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