From owner-chemistry@ccl.net Thu Jul  5 10:38:01 2018
From: "David Wahl dmwahl%x%eagles.usi.edu" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: Amber Force Field Nomenclature
Message-Id: <-53371-180705103357-18113-OOLstkh0K2raMBYOtMyvSw(a)server.ccl.net>
X-Original-From: "David  Wahl" <dmwahl(a)eagles.usi.edu>
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