From owner-chemistry:~at~:ccl.net Thu Jul 5 10:38:01 2018 From: "David Wahl dmwahl%x%eagles.usi.edu" To: CCL Subject: CCL: Amber Force Field Nomenclature Message-Id: <-53371-180705103357-18113-OOLstkh0K2raMBYOtMyvSw(a)server.ccl.net> X-Original-From: "David Wahl" Date: Thu, 5 Jul 2018 10:33:55 -0400 Sent to CCL by: "David Wahl" [dmwahl#eagles.usi.edu] Hello, I am using GROMACS to run a molecular dynamics simulation on a strand of methylated DNA. I have chosen the AMBER-99SB-ILDN force field with the bsc0 (from Perez, et al.) and CUFIX (from Yoo and Aksimentiev) parameters added. Within the dna.rtp file of the forcefield, there are several abbreviations indicating the residues. I understand that DG, DT, DC, and DA stand for the regular bases and DT5 or DT3 represent terminal bases. However, I am not sure what DM, DMJ, DMN, DCJ, DAN, etc. stand for. Looking at the atoms within the DM residues show that they are methylated, but I still want to make sure I am choosing the right residue and therefore know exactly what each of these might stand for. I really appreciate any insight! David