AMBER Archive (2009)
Subject: [AMBER] Generating LeAP file for helix containing non-standard amino acid
From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
I am having issues generating an amber force field for a protein containing my non-standard amino acid. I generated the helix itself in Macromodel and then modified the amino acid to my side chain (Cysteine -> Cys + side-chain, labeled DMV in this model).
I tried changing HETATOM to ATOM and moving the terminal residue to the end, but it didn't seem to significantly help (although it did try to compile the force field before giving an output of "Error: cannot run "path -j full - I ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit.
Attached is the PDB file as generated by Macromodel.
Thanks for any suggestions/help.