- Posts: 4
secondary structure number codes of CG protein
- sxn
- Topic Author
- Offline
- Fresh Boarder
Less
More
5 years 6 months ago #7813
by sxn
secondary structure number codes of CG protein was created by sxn
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
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
Please Log in or Create an account to join the conversation.
- sxn
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 4
5 years 6 months ago #7814
by sxn
Replied by sxn on 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", #@#
}
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", #@#
}
Please Log in or Create an account to join the conversation.
Time to create page: 0.086 seconds