[gmx-users] find the relevant structure out

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Tue Nov 23 06:33:46 CET 2010

I really do not know how to get those beta-sheet structures out,
or maybe by which ways?

Any clues are warmly welcomed and appreciated.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Sunday, November 21, 2010 11:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] find the relevant structure out

On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:

I had done 10ns simulation,

by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix.

there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets.

After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive.

Or maybe some parts I understand wrong.

Thanks for any advice and if I am wrong please let me know,

We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from "you are looking at the wrong files", to "pymol's definition of a beta sheet doesn't agree with dssp".

If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-)

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