normal secondary structure number codes of CG protein

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2 months 3 weeks ago #7813 by sxn
sxn created the topic: secondary structure number codes of CG protein
Hello,

I am coarse-graining a protein with sequence:
GDSWLKKFTEACNAAKGLEWVSNKISKFIDWLKEKIIP

The secondary structure file (.dssp) of the protein shows:
CCSTTHHHHHHHHHHTTHHHHHHHHHHHHHHHHTTSCC

On using martinize.py or charmm-gui, I get a coarse-grained Protein.itp file which says:
; Sequence:
; GDSWLKKFTEACNAAKGLEWVSNKISKFIDWLKEKIIP
; Secondary Structure:
; CCSTT1111HH2222TT1111HHHHHHHH2222TTSCC

I am not sure what do numbers 1 and 2 mean.
Can someone please suggest how is MARTINI interpreting "H" as numbers 1 and 2.

Many thanks in advance.

Best,
sxn

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2 months 3 weeks ago #7814 by sxn
sxn replied the topic: secondary structure number codes of CG protein
I figured out the answer to my question, the martinize.py script states:

ss_names = {
"F": "Collagenous Fiber", #@#
"E": "Extended structure (beta sheet)", #@#
"H": "Helix structure", #@#
"1": "Helix start (H-bond donor)", #@#
"2": "Helix end (H-bond acceptor)", #@#
"3": "Ambivalent helix type (short helices)", #@#
"T": "Turn", #@#
"S": "Bend", #@#
"C": "Coil", #@#
}

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