Francesco Pietra <chiendarret.gmail.com> wrote:
> On Sat, Jun 9, 2012 at 6:51 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).
>
> Thanks a lot. I'll firts try adding in smaller stocks. I am really
> interested to work at marine-like salt concentrations.
>
> However, what I can't understand is why the protein-complex (the
> ligand is innocuous to this regard) is not placed at its center of
> mass within the box (after I posted, I tried also without any
> counter-ion added). The complex is placed with one of its corners at
> the center of the box. This makes the box with one very short side,
> which does not comply with the nearly globular protein. I looked for
> bugs in the pdb file but found none (accurate renumbering from 1
> continuously both atoms and residues did not help).
This one I don't have a theory for.
Bill
>
> thanks
>
> francesco pietra
> >
> > Bill
> >>
> >> thanks for advice
> >>
> >> francesco pietra
> >>
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> >
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Received on Sat Jun 09 2012 - 11:00:03 PDT
