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non-standard peptide link

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  • Ben
    Good afternoon - I have been struggling a few days to get this to work: I want to create a cyclic peptide but through the side chain of the N-term and C-term
    Message 1 of 1 , Sep 9, 2013
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      Good afternoon -

      I have been struggling a few days to get this to work:

      I want to create a cyclic peptide but through the side chain of the N-term and C-term residues.

      For example. Here is my pdb:

      ATOM 1 N GLU 1 -0.517 -2.346 -1.038 1.00 0.00 N
      ATOM 2 CA GLU 1 0.042 -0.997 -1.038 1.00 0.00 C
      ATOM 3 C GLU 1 1.551 -1.037 -1.038 1.00 0.00 C
      ATOM 4 O GLU 1 2.188 -1.798 -0.295 1.00 0.00 O
      ATOM 5 CB GLU 1 -0.481 -0.212 0.199 1.00 0.00 C
      ATOM 6 CG GLU 1 -0.006 1.273 0.310 1.00 0.00 C
      ATOM 7 CD GLU 1 -0.430 2.077 1.525 1.00 0.00 C

      ...


      ATOM 67 NZ LYS 5 11.300 12.028 -0.443 1.00 0.00 N1+
      ATOM 68 H LYS 5 11.652 4.068 0.629 1.00 0.00 H
      ATOM 69 HA LYS 5 12.157 5.723 -1.937 1.00 0.00 H

      ...

      The bond would be between 1-GLU CD atom and the 5-LYS NZ atom (MS studies use EDC as a zero length cross-linker and uses the GLU and LYS side chains to create a peptide bond). This is analogous to creating a "patch pept".

      So I copied the "PRESidue PEPT" in the topology file and made this:

      PRESidue EKCYC

      ADD BOND -CD +NZ

      ADD ANGLE -CE -CD +NZ
      ADD ANGLE -OE1 -CD +NZ
      ADD ANGLE -CD +NZ +CE
      ADD ANGLE -CD +NZ +1HZ

      ADD DIHEdral -CD +NZ +CE +CD
      ADD DIHEdral -NZ -CE -CD +NZ
      ADD DIHEdral -CE -CD +NZ +CE

      ADD IMPRoper -CD -CE +NZ -OE1 {planar -C}
      ADD IMPRoper +NZ -CD +CE +1HZ {planar +N}

      END {EKCYC}

      in my generate.inp I added:

      patch ekcyc refe=-=(resid 1) refe=+=(resid 5) end

      when i run this I get the following errors:

      CNSsolve>patch ekcy
      PATCH> reference=1=(resid 1)
      SELRPN: 10 atoms have been selected out of 54
      PATCH> reference=2=(resid 5)
      SELRPN: 13 atoms have been selected out of 54
      PATCH>end
      %PATCH-ERR: to be deleted bond -CD +NZ not found in molecular structure.
      ...

      Any thoughts as to why I would be getting "not found in molecular structure" errors? The atoms it is mentioning are in the pdb and mtf file.

      Many thanks in advance

      Ben
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