> Actually the crystal structure of the pdb originally had three K+ ions. I
> have removed the K+ ion at residue 23 and saved the pdb file for my use, as
> a result my initial pdb file(1kf1_w.pdb) has K+ ions at residue no.24 and
> 25.
The AMBER prmtop setup programs renumber the residues sequentially, so if
you removed a residue, :24 will become :23, and :25 will become :24.
However, in many cases in solution, even at tight protein/DNA interfaces,
water and ions exchange positions on a ns- timescale. Therefore, it is
somewhat unlikely that the ion will not exchange. There are a couple of
ways to look for ion density at the site of interest. See the AMBER list
post that just came up regarding the grid command. A second option is to
use the hbond facility. For example, to see both residues :23 and :24 and
all ions to perhaps a particular carbonyl, :18.O
trajin traj.1
center :1-22 mass origin
image origin center familiar
donor mask :18.O
acceptor mask :23 :23
acceptor mask :24 :24
hbond series hb-series out hbond.out time 1.0 distance 3.2 angle -1.0 \
solventacceptor K+ K+ K+
See the new AmberTools manual at ambermd.org for more discussion...
--tec3
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Received on Tue May 25 2010 - 09:00:11 PDT
