AMBER Archive (2000)

Subject: Simulation of DNA

From: Marcela Madrid (mmadrid_at_psc.edu)
Date: Fri May 26 2000 - 12:58:19 CDT

Hi,

Is the most accurate way to simulate DNA in water, with PME,
constant P and T and counterions, to use parm98.dat?
Will this give substantially different results than using parm94?

if so, how do I do that? I copied leaprc into my directory
and replaced parm94 by parm98, is anything else needed?
Does the following stay the same: ?
loadOff all_nucleic94.lib
#
# Load main chain and terminating
# amino acid libraries.
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
loadOff ions94.lib

thanks, Marcela