Re: FEP, IONS, DUMMY atoms, LARGE numbers

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Tue Apr 18 2006 - 08:57:03 CDT

Raul,

> - I have only one Na+ ion present which should dissapear or become a
> dummy isnt it?

as I mentioned it before, one possible route to perform this alchemical
transformation is to grow a sodium ion as the neutral His residue is
being mutated into a negatively charged Asp.

> - should I fix both the Na+ and the Dummy in the same coordinates?

Fixing the sodium ion will ensure that it does not come too close to
the transformed residue, which may be desirable if your simulation is
too short to capture the formation and dissociation of the Asp-...Na+
ion pair.

> - Why even if a do so still large numbers appear?

In such transformations, the free energy is driven by the solvation of
charged species, which is inherently large. To convince yourself, take
a simple Born model for a rough estimate of the electric contribution
to the hydration free energy of sodium.

Now it is possible also that your hybrid topology be incorrect due to
missing exclusions. I am enclosing the His to Asp topology from the
library of hybrids that we will include on the Namd website shortly.
I suggest you use the latter in conjunction with PSFgen and Jerome
Henin's alchemify utility to clean out your PSF file.

> - should I use an harmonic potential to restraint some positions between
> tha atoms of the hybrid?

Soft positional restraints should do the trick.

Chris Chipot

RESI H2D -1.00
GROUP
ATOM N NH1 -0.47
ATOM HN H 0.31
ATOM CA CT1 0.07
ATOM HA HB 0.09
GROUP
ATOM CBA CT2 -0.09
ATOM HB1A HA 0.09
ATOM HB2A HA 0.09
ATOM ND1A NR1 -0.36
ATOM HD1A H 0.32
ATOM CGA CPH1 -0.05
GROUP
ATOM CE1A CPH2 0.25
ATOM HE1A HR1 0.13
ATOM NE2A NR2 -0.70
ATOM CD2A CPH1 0.22
ATOM HD2A HR3 0.10
GROUP
ATOM CBB CT2 -0.28
ATOM HB1B HA 0.09
ATOM HB2B HA 0.09
ATOM CGB CC 0.62
ATOM OD1B OC -0.76
ATOM OD2B OC -0.76
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND N HN
BOND N CA
BOND C CA
BOND C +N
BOND CA HA
BOND O C
BOND CBA CA
BOND CGA CBA
BOND ND1A CGA
BOND CE1A ND1A
BOND NE2A CD2A
BOND CBA HB1A
BOND CBA HB2A
BOND ND1A HD1A
BOND CD2A HD2A
BOND CE1A HE1A
BOND CGA CD2A
BOND CE1A NE2A
BOND CBB CA
BOND CGB CBB
BOND OD2B CGB
BOND CBB HB1B
BOND CBB HB2B
BOND CGB OD1
IMPR N -C CA HN C CA +N O
IMPR ND1A CGA CE1A HD1A
IMPR CD2A CGA NE2A HD2A
IMPR CE1A ND1A NE2A HE1A
IMPR ND1A CE1A CGA HD1A
IMPR CD2A NE2A CGA HD2A
IMPR CE1A NE2A ND1A HE1A
IMPR CGB CBB OD2B OD1B

_______________________________________________________________________

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex

                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr

     Science without management is worse than management without science

                                                        N. G. van Kampen
_______________________________________________________________________

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