Sorry, I had overlooked the option of changing residue name. So, what only remains is whether there is a tool for quicker capping. thanks francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Fri, May 2, 2014 at 6:51 PM Subject: patching ACE NME To: chimera <chimera-users@cgl.ucsf.edu> Hello; In parameterizing a new metal cluster, I would like to patch the various amino acids (which stand isolated from one another) with what are called by AMBER ACE and NME. I would like to do that within the whole block, not for each amino acid isolated from the block. Also, I would like to avoid tleap, which gets into troubles here. I could do that by modifying structure, but a problem arises of residue names, i.e, the original residue takes the name ACE or NME, or viceversa the capping groups take the name of the amino acid being capped. Is there a specific tool with chimera? thanks francesco pietra