Hello everyone,
I am trying to make a cyclic peptide (CYS LYS LEU … MET CYS) where there is a disulphide bond between S of the CYS residues at both ends. This is how I proceed.
1. I copied leaprc.ff12SB to my working directory and I excluded these lines from addPdbResMap { part of it:
# { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }:
2. I make the peptide with this command. I change CYS to CYX since we need to remove one H from each S in the CYS to make the disulphide bond possible.
peptide = sequence { CYX LYS LEU … MET CYX }
3. Then I manually make the bond between the S of the two CYS residues.
bond peptide.1.SG peptide.9.SG
4. After edit in the xleap this is what I got (please check the figure attached).
Could you please help me to make this cyclic peptide properly?
Thank you very much.
Best regards,
Maral
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Received on Thu Apr 21 2016 - 14:00:03 PDT
