[AMBER] Fwd: LEaP misplaces ions

From: Francesco Pietra <chiendarret.gmail.com>
Date: Sat, 9 Jun 2012 10:48:35 +0200

Hi:
While the description below is correct, I must add that already at
the neutral stage the protein-comples is out of the center of the box,
although the neutralizing Na+ are homogeneously placed around the
protein.

fp


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Sat, Jun 9, 2012 at 10:29 AM
Subject: LEaP misplaces ions
To: AMBER Mailing List <amber.ambermd.org>


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?

thanks for advice

francesco pietra

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Received on Sat Jun 09 2012 - 02:00:02 PDT
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