Hi Robin:
addIonsRand worked nicely (Na+ 227 Cl- 200 2). Now, in the final pdb,
Na+ and Cl- appear alternatively, one after the other one, rather than
a complete list of Na+ followed by a complete one of Cl-.
I am still perplexed why the protein-complex is misplaced within the
water box, but this is a different problem.
Also, I have some problems with the several Ca++ ions ligated to the
protein. The less ligated one flies away during equilibration (during
previous run). But this is still another problem, and a known one with
doubly-charged ions (I used the simple concanavalin-type
parameterization).
I still have to minimize-equilibrate the system, but before that I
want to clarify the issue of the position of the protein complex
within the box.
Thanks a lot
francesco
On Sun, Jun 10, 2012 at 9:11 AM, Robin Betz <rbetz.ucsd.edu> wrote:
> Hi Franceso,
>
> The command you're looking for is addRandIons:
>
> addIonsRand unit ion1 #ion1 [ion2 #ion2] [separation]
>
> UNIT _unit_
> UNIT _ion1_
> NUMBER _#ion1_
> UNIT _ion2_
> NUMBER _#ion2_
> NUMBER _separation_
>
> Adds counterions in a shell around _unit_ by replacing random solvent
> molecules. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
> opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
> the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
> If _separation_ is specified, ions will be guaranteed to be more than that
> distance apart in Angstroms.
>
> Ions must be monoatomic. This procedure is much faster than addIons, as
> it does not calculate charges. Solvent must be present. It must be possible
> to position the requested number of ions with the given separation in the
> solvent.
>
> This will replace randomly chosen solvent molecules with ions, so make sure
> that you have added enough solvent to the system.
>
> Robin Betz
>
>
> On Sat, Jun 9, 2012 at 11:09 PM, Francesco Pietra <chiendarret.gmail.com>wrote:
>
>> On Sat, Jun 9, 2012 at 7:26 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>> > Another hint is to look into the new(er) random ion command in leap which
>> > Robin Betz added as an alternative to addIons.
>> >
>> > I think it's described in the manual
>>
>> I was unable to trace a command "random ion" or "randomion", nor
>> anything similar under Robin Bertz in leap (manual ambertools12). I
>> only noticed "randomizeions" in cpptraj, but it does not seem to meet
>> the case.
>>
>> thanks
>> francesco pietra
>> >
>> > HTH,
>> > Jason
>> >
>> > On Sat, Jun 9, 2012 at 12:51 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> >
>> >> On 6/9/2012 1:29 AM, Francesco Pietra wrote:
>> >> > Hi:
>> >> > Adding ions to a regular protein-single-residue-small-molecule ligand
>> >> > of ca 260 residues (built through autodock from previously
>> >> > equilibrated protein, a procedure familiar to me, normally without
>> >> > problems) results in the protein not being centered in the TIP3P box.
>> >> > This is caused by a ball-like group of 27 Cl- ions, with one Na+ at
>> >> > the center, lying outside the protein surrounded homogeneously by Cl-
>> >> > and Na+. The aim was to get a ca 0.6 M NaCl concentration
>> >> >
>> >> > Commands executed with ambertools12 LEaP:
>> >> >
>> >> > -- xleap ....leaprc.ff12SB
>> >> >
>> >> > -- source leaprc.gaff
>> >> >
>> >> > -- prep and params for frcmod.ionsjc_tip3p, calcium++ (6 present,
>> >> > bound to the protein, and retaining their position on protein
>> >> > equilibration), and ligand.
>> >> >
>> >> > -- loadpdb (two identical models).
>> >> >
>> >> > -- solvate box model1 TIP3BOX3P 12 0.85 (added 23545 waters;
>> >> > dimensions 107, 118, 69; vol 876953 A^3).
>> >> >
>> >> > -- solvateoct model2 TIP3PBOX 12 0.85 (added 39438 waters; vol 1315698
>> >> A^3).
>> >> >
>> >> > -- for both models: neutralize (addions Na+ 0, as the protein complex
>> >> > has charge -27.00000), then "addions Na+ 200" "addions Cl 200".
>> >> >
>> >> > -- saveamberparm ...
>> >> >
>> >> >
>> >> > -The ligand, treated by antechamber, had RESP charges.
>> >> >
>> >> > I carried out the above with either the protein retaining its crystal
>> >> > water, or not. Same problem. I repeated everything from scratch with
>> >> > newly equilibrated protein, with same problems.
>> >> > Minimization/equilibration does not correct; actually it emphasizes
>> >> > the problem, making one side of the box even more disequilibated.
>> >> >
>> >> > I wonder why those misplaced Cl- (and one Na+) have replaced water
>> >> > molecules inhomogeneously around the protein. Was the number of added
>> >> > ions too large for the water molecules present?
>> >> When I wrote the addIons code, I didn't think to test such high
>> >> concentrations. I know of one other bug in addIons that is easier to
>> >> test for and is relatively innocuous: adding 2 Cl- to an Na+ does not
>> >> give a linear arrangement.
>> >>
>> >> The code uses an octree data structure (each cube divides into 8 smaller
>> >> cubes recursively) to optimize space; it is possible the bug is due to
>> >> an error in pointer arithmetic for the data structures involved. Using
>> >> memory-checking instrumentation like Purify might help.
>> >>
>> >> It may be possible to work around it by adding smaller amounts of ions
>> >> with each command more times, or more simply by following the less
>> >> recommended approach of addions before solvate (creates more vdw voids
>> >> by placing ion then removing potentially a few waters).
>> >>
>> >> Bill
>> >> >
>> >> > thanks for advice
>> >> >
>> >> > francesco pietra
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
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>> >>
>> >
>> >
>> >
>> > --
>> > 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
>>
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Received on Sun Jun 10 2012 - 04:00:03 PDT
