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
>> >
>> > _______________________________________________
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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 - 23:30:03 PDT
