AMBER Archive (2009)

Subject: [AMBER] ptraj randomizeions

Date: Tue Apr 07 2009 - 18:32:23 CDT

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,

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