Try using "addIonsRand" instead of "addIons". Does that work? (Note, it
adds ions in random positions rather than according to electrostatic
potential).
HTH,
Jason
On Mon, May 6, 2013 at 9:35 PM, Johannes Zuegg <j.zuegg.uq.edu.au> wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 06 2013 - 20:30:02 PDT
