normal error: invalid command name "La::mevsvd_br" during secondry str. analysis

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1 year 2 months ago #7663 by cm
hi,
i am trying to analyse the secondary structure in vmd.when i am using this command
source cg_secondary_structure.tcl
and arter that
cg_helix {{5 48} {120 146}} -hlxmethod "cylinder" -hlxcolor "red" -hlxrad 2.5
the error is
invalid command name "La::mevsvd_br"
how i will solve this problem.
thanking you

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1 year 2 months ago #7671 by cm
can i do this secondary structure analysis in gromacs by do_dssp command.
pls give me some idea about the martini protein cg secondary.
thanking you

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1 year 1 month ago #7675 by cm
wheather in case of martini protein cg the secondary structure of proteins remain fixed and also the helix changes during the simulation.

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1 year 1 month ago #7677 by peterkroon
The secondary structure of proteins in Martini is fixed, and does not change. So it's the same as in the atomistic protein you gave to martinize.
If you want to see secondary structure chagnes in proteins you can't use Martini.

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1 year 1 month ago - 1 year 1 month ago #7678 by cm
Thanks for your quick reply.if secondary structure does not change...Then if I only want the secondary structure of protein(initial).Then what should l do .
Last edit: 1 year 1 month ago by cm.

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