AW: A larger protein data bank for performance benchmark

From: Norman Geist (
Date: Tue May 14 2013 - 10:30:08 CDT




Norman Geist.


Von: [] Im Auftrag von Rebecca Swett
Gesendet: Dienstag, 14. Mai 2013 03:52
An: linux freaker
Cc: Ajasja Ljubetič; Namd Mailing List
Betreff: Re: namd-l: A larger protein data bank for performance benchmark


I think you are being somewhat unclear. Are you looking for the PDB structure of a large protein? or are you looking for a large set of PDB's?
The acronym PDB stands for protein data bank, is the repository of known crystal structures. Used as a file extension, it represents
crystallographic coordinates saved in the standardized protein data bank format. is where you would find most known structure files in the downloadable format
of numbers and letters. For example 2aa1.pdb is the structure of the day today and is a large toxin. If you are looking for a collection of structure files in pdb format, you may want to look at some of the search and download options on that site. However I strongly suggest doing some more reading. It is imperative to good science that users understand the files and formats they are working with.

R.J. Swett
Wayne State University
357 Chemistry
Detroit, MI 48201
Lab Phone 313-577-0552
Cell Phone 906-235-0768

On 5/13/2013 8:51 PM, linux freaker wrote:

Hi All,

I looked into but couldnt get large size protein data bank. As I am new to NAMD, please suggest me larger PDB. is the link I tried looking into but those are samll size PDBs.

Can you please paste the link for large size PDB?

Also, is it possible to accomunlate and run ./namd2 src/* for selecting various PDBs?


On Mon, May 13, 2013 at 11:42 PM, linux freaker <> wrote:

Which shall I choose? can you suggest me a pdb just like alanin which I can use directly?

On 13 May 2013 22:43, "Ajasja Ljubetič" <> wrote:

Here is a ready to run benchmark (apo1) (Direct download <> )






On 13 May 2013 18:52, Cesar Millan <> wrote:


On Mon, May 13, 2013 at 11:49 AM, linux freaker <> wrote:

I installed namd on linux machine.I ran src/alanin on 4 processor and it completed in no time.I need it to take some 5-10 minutes running so that I can benchmark.where I can download pdb from which is larger in size?





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