Re: [apbs-users] Set correct grid values

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

Hello –

Can you please provide more information about what you are trying to calculate?  For most quantitative calculations (as opposed to visualization), it is a good idea to have the grid spacing less than 0.5 A (often ~0.25 A).  The grid length has a more complicated formula; I recommend using PDB2PQR to generate template input files that can recommend grid lengths.

Thanks,

--
Nathan Baker
Laboratory Fellow
Pacific Northwest National Laboratory
+1-509-375-3997
http://www.linkedin.com/in/nathanandrewbaker/

From: Javier Cáceres [mailto:ja...@gm...]
Sent: Friday, August 30, 2013 7:17 AM
To: apb...@go...
Subject: [apbs-users] Set correct grid values

Hello,

Im new on apbs. I want to make electrostatic binding energy calculations, and a have doubts on what are good values for the grid dimensions.
I really want to know when my calculations are set in the right way, and the values that a put in the input file are the corrects for my protein.
For example, I don't understand what dime values are the best for my protein. A put 321 321 321 and I get a result, but when a put 289 257 289 a get other. Wich one is the best? How do I know?

Thanks,

Javier.