AMBER Archive (2002)

Subject: memory allocation in mm_pbsa

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Wed Sep 11 2002 - 05:41:04 CDT

Dear all,
I am using mm_pbsa to post-process a trajectory file made with sander
(amber7)
using explicit solvent and PBC (about 41000 total atoms). The script
invokes sander to calculate the
MM part, but my sistem is too big to get sander working:
 Failed to allocate memory for ipairs: 865675245 (I am using
-DMEM_ALLOC)
This is because the sander input created by mm_pbsa has a cut-off larger
than
the system size (99999.0) and there are too many non-bonded pairs.
I am using a Fuel R14000, 512Mb
Thank you very much in advance for the reply
Giulio 

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Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
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tel 0039-059-2055145
fax 0039-059-2055131
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