Hi all,
I know the issue has been raised several times, but I am unable to find a good solution in the Archives.
I am trying to add salt to a Protein/DNA complex (as per XRay structure) using the tleap script (AmberTools v13):
source leaprc.ff99SB
m01 = loadPdb ProtDNA.pdb
check m01
solvateoct m01 TIP3PBOX 12
addions m01 Na+ 0
# 200mM NaCl based on 10,438 water molecules in the box
addions m01 Na+ 38 Cl- 38
But in most cases I get a few of the Na+ or Cl- atoms with "No solvent overlap", which are located outside the solvent box (by visual inspection)
...
>Placed Na+ in m01 at (7.58, -37.85, 6.65).
>(No solvent overlap)
The only workaround I found is to "play" around with the size of the solvent box, i.e. in this model when I use:
10A and 30 NaCl => OK: all Na+ and Cl- with "Replacing solvent molecule" and inside the waterbox
12A and 38 NaCl => one Na+ and Cl- with "No solvent overlap" and outside the waterbox
12.5A and 40 NaCl => OK: all Na+ and Cl- with "Replacing solvent molecule" and inside the waterbox
13A and 42 NaCl => several Na+ and Cl- with "No solvent overlap" and outside the waterbox
(number of Na+/Cl- is based on 200mM NaCl and the number of water in the box)
In all cases the addions reports similar values:
>Grid extends from solute vdw + 9.72 to 15.82 (for 10A)
>Grid extends from solute vdw + 10.86 to 16.96 (for 12.5A)
>Resolution: 1.00 Angstrom.
[Q]: Is there a better way to control the addions command in tleap?
In case it works (10A and 12.5A), most addional Na+ Cl- are "cuddled" together in an area of the waterbox,
so I am using randomizeions in ccptraj to "spread" them around.
[S]: Would be nice to have such a command in tleap however!
Cheers
Johannes
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Received on Mon May 06 2013 - 19:00:02 PDT
