I have added an acetyl group to the N-terminus of a peptide using CHARMM-GUI's PDB reader. I uploaded a PDB of the peptide and then get to the "Manipulate PDB" page, then I used "Terminal Group Patching" and selected the option which corresponds to an acetylated N-terminus. It output a PDB with the modified N-terminus (all output files are attached, Sursi4charge.orig.pdb is the original input pdb).
I used the "Terminal Group Patching" to add "ACE" and "CT2," but if I run the modified peptide on GROMACS' CHARMM36 using pdb2gmx, I get the error "Fatal error: Atom CAY in residue MET 1 was not found in rtp entry MET with 18 atoms while soring atoms."
I believe the issue I'm having is due to my rtp lacking entry of the terminus residue, but I do not know how I can derive the parameters for the residue.
I would really appreciate if anyone can share some experiences on solving this issue!
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