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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
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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 - 00:30:03 PDT
