Date: Wed, 20 Mar 2019 05:08:42 +0000 (UTC)
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 https://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/01-vmd-tutorial/html/node2.html .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.
Thanks and Regards,
Saikat Pal
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