From owner-chemistry@ccl.net Tue Nov 7 13:52:01 2006 From: "Sandeep Kumar kumarsan(_)jhu.edu" To: CCL Subject: CCL: MD simulations using MMFF94x and MOE Message-Id: <-32955-061107133645-19111-9/BO6zVaZTSJV6IXPsFC1g(~)server.ccl.net> X-Original-From: "Sandeep Kumar" Date: Tue, 7 Nov 2006 13:36:44 -0500 Sent to CCL by: "Sandeep Kumar" [kumarsan],[jhu.edu] Dear Members: I am trying to do MD calculations on a 28 residue peptide using MMFF94X forcefield as implemented in MOE to assess its conformational flexibility. I was wondering if somebody has experience of using MMFF94x forcefield for peptide simulations and how does it compare with other forcefields, say, AMBER or CHARMM? Another related question whether to do implicit solvation or explicit solvation simulations? I mean which is better and usually what should be the time scales for such simulations? Any advices shall be greatly appreciated. Yours sincerely, Sandeep Kumar ----------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan!^!jhu.edu. URL: https://jshare.johnshopkins.edu/skumar23/public_html/ Previous URL: http://www.lecb.ncifcrf.gov/~kumarsan