Re: [AMBER] Ptraj cluster error

From: Thomas Cheatham <>
Date: Mon, 4 Aug 2014 09:21:28 -0600 (MDT)

> trajin ../PknGAde_md_reimage20ns.mdcrd
> cluster out PknGAde20ns representative pdb average pdb all amber averagelinkage clusters 5 rms :247 <:5.0
> Ptraj exited with the following error message:
> ERROR in safe_malloc: Error in alloc of -2021047296 bytes

This is usually overflow meaning that you are trying to allocate too much
memory, which suggests that you are choosing too many frames to cluster.
As the clustering does a full pairwise comparison, you essentially need
N**2 memory if you have N frames. To get around this, use the sieve
option to cluster less frames on the first pass (when doing the initial
pairwise comparison); the second pass will go over all frames. A good
initial guess is on the order of ~500-5000 total frames, so, if N frames,
choose sieve N/1000 or so...


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Received on Mon Aug 04 2014 - 08:30:03 PDT
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