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

  • cm
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9 months 2 weeks ago #7689 by cm
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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7 months 3 weeks ago #7745 by songhd
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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