Hi,
In addition to Jason's suggestion, if you can also try adding ions 1
at a time, e.g.
addions m01 Na+ 1
addions m01 Na+ 1
...
addions m01 Cl- 1
It will be slower than addIonsRand but will use electrostatic
potential when determining placement.
-Dan
On Mon, May 6, 2013 at 9:19 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue May 07 2013 - 08:00:02 PDT
