CCL: Amber Force Field Nomenclature

From: "David Wahl" <dmwahl(a)eagles.usi.edu>
Subject: CCL: Amber Force Field Nomenclature
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