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.
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
> >
> > _______________________________________________
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> > 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
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Received on Sat Jun 09 2012 - 10:30:03 PDT
