Hi,
I'm running some simulations of DNA (canonical B-form) using amber with the
parmbsc0 parameter set. Everything seems to work fine, but I've noticed
that I get different results depending on whether I use tleap or sleap for
my initial system set-up. Specifically, I've noticed that the dihedral
angle distributions I get are different (most noticeably for delta and the
pseudorotation phase angle). The distributions I get when my system is set
up with tleap look the same as those in the supplementary material of the
original parmbsc0 paper - the distributions I get with sleap do not.
If anyone can give me any clues as to why these differences occur/what I am
doing wrong, it would be very much appreciated. My leap input looks like:
source leaprc.ff99bsc0
dna1 = loadPdb 1BNA_no_waters.pdb
saveAmberParm dna1 1bna_99.prmtop 1bna_99.prmcrd
addions dna1 Na+ 0
saveAmberParm dna1 1bna_99_ions.prmtop 1bna_99_ions.prmcrd
solvateoct dna1 TIP3PBOX 8.0
saveamberparm dna1 1bna_99_ions_octbox8.prmtop 1bna_99_ions_octbox8.inpcrd
quit
And everything about my simulations is identical, except that in one case I
use tleap and in the other I use sleap.
Thanks a lot for your help,
Chris
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Received on Tue May 15 2012 - 03:00:04 PDT
