AMBER Archive (2006)

Subject: AMBER: MM-PBSA memory usage

From: Stefano Pieraccini (
Date: Thu Oct 26 2006 - 07:33:41 CDT

Hi all,

I am using MM-PBSA to calculate binding energy between two proteins in a complex. I suxeeded in this and was able to claculate the total binding energy using as much snapshots as I wanted. As i tried to decompose the energies in a pairwise fashion, in order to find the residues more strongly interacting, I could only perform the calculation selecting small groups of a.a. on the different subunits and using only up to 20 snapshots, because the program crashed running out of memory. I used the MM-PBSA of amber9 on a AMD athlon processor pc with 2 GB RAM. The protein complex was composed of approximately 800 a.a. in total. Even using groups of 20 a.a. on each of the two subunits and only 20 snapshots the program run out of memory. With 10 snapshots it worked. Is it normal such a big mamory usage by the program in the pairwise decomposition or should I think there is someting wrong in the setup?

Thank you in advance

Stefano Pieraccini

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