Hi,
On Wed, Mar 20, 2019 at 1:09 AM Saikat Pal <saikatpaliitg.yahoo.com> wrote:
>
> Dear all,I am confused regarding secondary structure character notation or SS type (Amber manual 18 pp 689). Here E = parallel beta sheet and B = anti-parallel beta sheet, but in VMD E = extended beta sheet and B = isolate bridge beta
I'm going to punt responsibility on this a bit - cpptraj uses 'E' and
'B' to specify secondary structure in this way
(parallel/anti-parallel) because this is how it had originally been
implemented in ptraj, and I was aiming to preserve backwards
compatibility. This has the upside of making it easier to distinguish
between the two beta sheet types, but is not in keeping with the
original usage as defined by Kabsch & Sander in the original DSSP
paper. It may be worthwhile to add a keyword to cpptraj DSSP that
brings the output more in line with the original paper.
> I have analyzed the same trajectory using both amber and VMD package. And the results are very much opposed to each other. I have attached both the secondary structure analysis.
The picture from VMD was very poor resolution, but it seems that VMD
orders residues from the top down while cpptraj does it the other way,
so simple visual inspection isn't very easy. I'll try to do some
comparisons on my own.
Thanks for the report,
-Dan
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Received on Wed Mar 20 2019 - 05:30:02 PDT
