I was asked to summarize my reponses about the van der Waals radii of Zn.
Below is first my question - and then the responses. Thanks to everyone
who responded! Hello. I am interested in obtaining the AMBER forcefield
parameters R* and epsilon (van der Waals radii and well depth) for Zn to
run a MD simulation. Does anyone have these parameters or approximations?
J. Aqvist parameterized the alkali and alkaline earth metals by performing
free energy pertubation simulations in aqueous solution. He calculated the
A and B values necessary to obtain the AMBER van der Waals radii
parameters (J. Phys. Chem. 1990, 94, 8021-8024). If anyone has done
a similar simulation with Zn, please contact me.
Hi, Kenneth Merz and coworkers have done many simulations on Zn
metalloenzymes using AMBER forcefield. Their Zn2+ parameters were
published in JACS in 1991(Hoops, SC, Anderson, KW, Merz, KM, Jr. JACS
1991, 113, 8262). There are others in the literature that work equally
well with AMBER. Yajun Zheng
Actually, Aqvist's parameters are arbitrary: multiple combinations of R* &
epsilon give the same results. See Ross & Hardin (JACS 116, 6070-6080
(1994)) to see a comparison and a formula for deriving R* for epsilon=0.1
for monovalent cations in TIP3 water, given the empirical ion-OW distance
from e.g. neutron diffraction. Note also the corrections needed when
'porting' from the "combining rules" that Aqvist used to the ones used for
amber, which has R*ij=Ri+Rj, eij=sqrt(ei*ej). Also, parameters derived for
single-vdw waters like TIP do not work for ion contacts with amber-type
atoms, since the OW is 'inflated' to include the HW's. This is also shown
in Ross & Hardin. Bill Ross Oops - the Ross & Hardin formula won't be
useful for +2 species, but the discussion should be useful; also see the
ions page at
http://amber.ch.ic.ac.uk/0Net/index.html Bill Ross
Dear Katherine, some years ago, I run some simulations on the catalytic
zinc ion in alchol dehydrogenase. Then, I collected the following list of
other Zn simulations. It is probably somewhat outdated now, but at least a
starting point. E Clementi et al. J. Chem. Phys 72(80)260
Non-bonded potential for Zn with H2O and CO2 A Vedani et al. J. Comp.
Chem. 7(86)701 A Vedani & DW Huhta, J. Am. Chem. Soc. 112(90)4759
Program Yeti; a special bonded potential for S, N and O ligands;
Simulations of carbonic anhydrase
R(Zn)=0.69 A; eps(Zn)=-0.014 kcal/mole KM Merz et al. J. Am. Chem. Soc.
113(91)406 SC Hoops et al. J. Am. Chem. Soc. 113(91)8262 KM Merz & L
Banci, J. Phys. Chem. 100(96)17414 KM Merz & L Banci, J. Am. Chem. Soc.
119(97)863
Simplified bonded potential for Amber with His, H2O and OH-;
Simulations of carbonic anhydrase
R(Zn)=1.1 A; eps(Zn)=0.0125 kcal/mole PMT de Kok et al. Recl. Trav.
Pays-Bas 107(88)355 NA Beijer et al. Ann. Ny Ac. Sci. 377(91)494
MM studies with Amber on alcohol dehydrogenase
R(Zn)=1.4 A; eps(Zn)=0.01 kcal/mole U Ryde, Proteins, 21(95)40-56 U
Ryde, Protein Science 4(95)1124-1132 U Ryde, J. Comp.-Aided Mol. Design
10(96)153-164
MM, MD, and QC/MM studies of the active site zinc ion in alcohol
dehydrogenase. Force field for Mumod and Amber
R(Zn)=1.1 A; eps(Zn)=0.0125 kcal/mole RH Stote & M Karplus, Proteins,
23(95)12-31
Non-bonded model for Zn proteins with AMBER
sigma(Zn)=1.95 A; eps(Zn)=0.25 kcal/mole; q(Zn)=+2 R Reddy, et al, J.
Am. Chem. Soc., in press.
FEP calculations with Amber on Adenosine Deaminase
R*=1.1 A, eps=0.1 kcal/mole, q(Zn)=+1.2 Best regards, Ulf dear
katherine maybe you find what you are looking for about Zn in
http://amber.ch.ic.ac.uk/0Net/ions mathy froeyen
Received on Fri Jun 08 2001 - 07:43:03 PDT
