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Cu2+ parameter
#15963 10/17/07 03:56 PM
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Hi,

I want to simulate a complex containing Cu2+ - I have not been able to find the parameter for Cu2+(does it exist?).

In order to estimate the LJ parameter should one proceed like Stote et al. ?

Re: Cu2+ parameter
greisen #15964 10/19/07 10:26 AM
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Hi again,

I have been looking into the parameters used by par_all27_prot_na.prm and especially for zinc how come that the LJ parameters for zinc used are:
ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
! RHS March 18, 1990
when the study by Stote et Karplus(1995) have estimated another sigma?

Re: Cu2+ parameter
greisen #15965 10/19/07 10:41 AM
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Stote&Karplus have not estimated another sigma, they have estimated sigma; the values in the CHARMM parameter files are however given as Rmin/2 (as is clearly indicated at the top of the NBONDs section of the parameter file) .


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Cu2+ parameter
lennart #15966 10/19/07 01:39 PM
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upps - really sorry forgot to converge from sigma to r( ) - a little advise on the Cu2+ - the Stote&Karplus would be the way in order to get good parameters for Cu2+?

Re: Cu2+ parameter
greisen #15967 10/20/07 03:20 PM
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I wouldn't assume that substitution for copper(II) with zinc(II) is appropriate, since copper is a real transition metal that varies in oxidation-state and ligand-geometry. Did you check the experimental hydration energy for copper(II)? Else google is an option (or HCP).

Re: Cu2+ parameter
jb007 #15968 10/24/07 07:37 PM
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I have found a recent paper(2006) where they have used parameters for Cu2+ - "Deng et al Biophysical Journal 2006" if anybody needs them I will post them here:

! Emin(kcal/mol) ! Rmin(A)
MCU 0.00 -0.060 1.380

MASS 96 MCU 63.546 Cu ! Copper


No zn2+ would be a bad solution for Cu2+.

CHARMM parameters for Silver and Gold
greisen #34802 02/16/15 02:40 PM
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Hi
Did you find parameters for Silver and Gold

Topology should be like:
-------------------
MASS 501 AG 107.86820 ! topology for Silver, Ag
MASS 502 AU 196.96656 ! topology for gold, Au
-------------------
and I found in a paper :
epsilon for Ag is -0.002541
epsilon for Au is -0.012793

(Griebel, Michael, Stephan Knapek, and Gerhard Zumbusch. extensions to more complex potentials and molecules, in "Numerical simulation in molecular dynamics: numerics, algorithms, parallelization, applications." Vol. 5. Springer Science & Business Media, 2007.:151-209)

what about the Rmin/2 for Ag and Au?

Bests
Kalani

Last edited by kalanimr; 02/16/15 02:43 PM.

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