normal secondary structure analysis after converting from coarse grained to all atom

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5 months 1 week ago #7689 by cm
cm created the topic: secondary structure analysis after converting from coarse grained to all atom
hi,
after converting the cg to aa structure of protein ,i want to calculate the secondary structure of protein.during this transformation i have choosen charmm force field.basically i have two protein and the residue number are written correctly but i want to name them as protein1 and protein2.how i will do this.is it possible then to calculate the secondary structure using charmm.
thanking you

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3 months 3 weeks ago #7745 by songhd
songhd replied the topic: secondary structure analysis after converting from coarse grained to all atom
1. You can set different chains, segnames such as chain A, chain B, segname A, segname B using VMD tcl script.

2. You can check the secondary structure from VMD - sequence viewer

Hyun

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