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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 09 2012 - 01:30:02 PDT
