Subject: Summary: Zn within AMBER

From: Harald Lanig <[email-masked]>
Date: Wed, 22 Jul 1998 08:45:49 +0200

-- 
---------------------------------------------------------------------
 Dr. Harald Lanig
 Computer Chemie Centrum der Universitaet Erlangen/Nuernberg
 Institut fuer Organische Chemie I, Naegelsbachstr. 25
 D-91052 Erlangen, Germany
 
 Phone +49(0)9131-85 6581  Fax -85 6565
 mailto:[email-masked]
 http://www.ccc.uni-erlangen.de/clark/lanig
---------------------------------------------------------------------

Dear Netters,

here are the (unchanged) answers to my question about Zn Parameters for AMBER.
Thanks to everybody who replied to me. 

-Harry

The original query:
Dear netters,

optimizing metalloenzymes (e.g. Zn) with AMBER needs parameters
not included in the original 95 parameter set.
Has anybody out there experiences about how to perform such
calculations?

Any help is highly appreciated!

The answers:
111111111111111111111111111111111111111111111111111111111111111111111
Takanori Kanazawa  
[email-masked]

    The following literature may help you.
(In the first two articles, modified version of AMBER force-field
 is used.)

1. W.C.Guida et al.  J.Comp.Chem.  13(2),214-228(1992)
2. C.McMartin et al. J.Comp-Aided.Mol.Design 11,333-344(1997)
3. S.C.Hoops et al.  JACS 113,8262-8270(1991)

"http://www.amber.ucsf.edu/amber/0Net/ions" also might help you.

2222222222222222222222222222222222222222222222222222222222222222222222
Ulf Ryde
[email-masked]

Dear Dr. Lanig,
I have performed quite a few simulations of metalloproteins (Cu, Zn)
with Amber as well as with other programs, and I have also performed
some studies of parameterisations and charge estimations nessesary for
such studies.

Some of my relevant references:
U. Ryde (1995) 
Molecular dynamic simulations of alcohol dehydrogenase with a varying  
coordination number of the catalytic zinc ion.
Proteins. Struct. Funct. Genet. 21, 40-56. 

U. Ryde (1995) 
On the role of Glu-68 in alcohol dehydrogenase.
Protein Science 4, 1124-1132. 

U. Ryde (1996) 
The coordination of the catalytic zinc ion in alcohol dehydrogenase  
studied by combined quantum chemical and molecular mechanical calculations.
J. Comput.-Aided Mol Design 10, 153-164.

K. Pierloot, J. O. A. De Kerpel, U. Ryde & B. O. Roos (1997) 
Theoretical study of the electronic spectrum of plastocyanin.
J. Am. Chem. Soc. 119, 218-226.

E. Sigfridsson & U. Ryde (1998) 
A comparison of methods for deriving atomic charges from the electrostatic 
potential and moments.
J. Comp. Chem.  19, 377-395.

J. O. A. De Kerpel, K. Pierloot, U. Ryde & B. O. Roos (1998) 
Theoretical study of the structural and spectroscopic properties of stellacyanin.
J. Phys. Chem. B,  102, 4638-4647.

J. O. A. De Kerpel & U. Ryde (1998) 
Protein strain in blue copper proteins studied by free energy perturbations
Proteins. Struct. Funct. Genet., submitted

Some other references on Zn:
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

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

3333333333333333333333333333333333333333333333333333333333333333333
John W. Cox
[email-masked]

Dr. Lanig,
I've done 2 years work on platinum-DNA containing systems, using a
derivative of the AMBER parameter set. Adding all the parameters for Pt
(including 2 new atom types, PT and NM) had to be done manually. I started
adding them into the parameter set used by HyperChem, and later into
Insight/Discover. The text references for HyperChem were a good place to
start, there are a few pages describing the addition of new atom types and
their corresponding values (stretch, bend, etc.).
As far as the values that will make up the additions for your
metalloenzymes, they may be available in the literature. I'm not directly
familiar with Zn values.
If this helps, and you would like more details, etc., feel free to email
me directly. 
There is also a Chem. Reviews article, Zimmer, M., Chem. Rev., 1995, 95,
2629 (I think this is the first page), that is a good reference.