AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa calculation allocation error

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Aug 21 2006 - 11:37:14 CDT

> Number of triangulated 3-point waters found: 0
>
> Grid dimension at level 2 199 211 163
>
> PB bomb in pb_saarc(): Allocation aborted 0 41 41
>
>My first question is about the meaning of this "Allocation aborted" error, what does that mean?
>
>
>
This means that you don't have enough memory on your computer to use 0.5
A grid in PB for your system. Please try 0.75 A or 1.0 A to see whether
you can run it.

>The second question is that whether I should worry about the "Number of triangulated 3-point waters found: 0" output in the third part, since I used an explicit solvent system during the simulation.
>
>
>
This is because you have stripped all waters, so 0 waters would be found.

>The last question is that, altough I solvated my system in a water box the .prmtop file does not contain any box info. Should I include the box info into the .prmtop file for the calculations, if yes how?
>
>
No. The box info is not used for any calculations in implicit solvents
in AMBER.

Ray 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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