Re: [Pdb2pqr-users] 70000 atom APBS calculation

[Baker, N. <Nat...@pn...>]

Hello --

Can you please provide the input file you're using for this calculation?

Thank you,

--
Nathan Baker
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling Group
Pacific Northwest National Laboratory
+1-509-375-3997
http://nabaker.github.io

From: Kotaro Kelley <kelleykk@MIT.EDU<mailto:kelleykk@MIT.EDU>>
Date: Wednesday, June 18, 2014 at 7:46
To: PDB2PQR-USERS mailing list <pdb...@li...<mailto:pdb...@li...>>
Subject: [Pdb2pqr-users] 70000 atom APBS calculation

Hi, I am trying to calculate an electrostatic calculation for a pdb structure containing 70000 atoms. I can run pdb2pqr fine from the command line. When I go to run apbs with this input file, the program tries to access way more than the 16 GB of ram available on my computer. This causes the computer to essentially freeze. If I leave it overnight, the process is killed by the OS or the program. Is there any work around to this problem? Is it possible to make an exception to the 10000 atom limit on the web servers? Thank you.