Dear all, I am trying to generate a psf file for a small (13 aa) cyclic peptide based on the template, "eginput/PSF_generation/genCircPep.py". However, it seems that it is not working: all HT1/HT2/HT3 and OT1/OT2 are still present in the generated psf file and from careful reading of the numbers of the bond definitions in the psf-file it seems that there is defined a bond between resi 1 C and resi 13 N (it should be the oposite). I appeared to be that the references in the patch definition should be swapped:
before: patch PEPT reference=-=(resid 1) reference=+=(resid 13) end after: patch PEPT reference=+=(resid 1) reference=-=(resid 13) end but after this change xplor complaints about missing bond parameters: %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%% bond energy constant missing. target bond length missing. ATOM1: SEGId=" ", RESId="13 ", NAME="C ", CHEMical="C " ATOM2: SEGId=" ", RESId="1 ", NAME="N ", CHEMical="NH3 " I hope someone can help me figure out this problem! best regards, Jakob -- Jakob Toudahl Nielsen, post doc Laboratory for Biomolecular NMR Spectroscopy inSPIN, Center for Insoluble Protein Structures Department of Chemistry, University of Aarhus Langelandsgade 140, DK-8000 Aarhus C, Denmark Phone: +45 871 55372 or +45 2993 8502 (cell)
