AMBER Archive (2009)

Subject: [AMBER] ptraj randomizeions

From: taufik.alsarraj_at_utoronto.ca
Date: Tue Apr 07 2009 - 18:32:23 CDT

Hi,
I would like to follow tutorial B3 "All Atom Structure Prediction and
Folding Simulations of a Stable Protein (Folding Trp-Cage Peptide)" to
examine the hydrogen bonding between a zipper and DNA.
i use this script in xleap
{ source leaprc.ff99SB
source leaprc.ff99bsc0
cebp = loadpdb CEBP.pdb
addions cebp Na+ 0
solvateoct cebp TIP3BOX 8.0
saveamberparm cebp CEBPinit.prmtop CEBPinit.inpcrd
}

then i should run
> ptraj CEBPinit.prmtop ranna
where ranna is
{
trajin CEBPinit.inpcrd
randomizeions @Na+ around:?? by 5.0 overlap 3.0
trajout CEBPinitranna.inpcrd restart
}

my question is: should the Na+ be around all protein and DNA residues
i.e. 1:154 or just around the DNA i.e. 115:154?

Many thanks,
Taufik

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber