Hi Hari,
> I have problems finding amber parameters and resp charge for iron (or
> zinc,
> which can be used to replace iron) in the molecule containing an iron
> atom
See
Ryde, U. Proteins: Struct., Funct., Genet. 1995, 21, 40.
Ryde, U. Eur. Biophys. J. Biophys. Lett. 1996, 24, 213.
Ryde, U. J. Comput.-Aided Mol. Des. 1996, 10, 153.
These have parameters for CHARMM for zinc in LADH. You can probably adapt
these parameters for your own needs although you will probably want to refit
your own parameters in the same way that Ryde does in these papers.
> and its ligands (octahedral structure) containing five amino acids. The
> structure was taken from the crystal structure 1AIJ and the amino acids
> were
> neutralized by adding extra amino or carboxyl groups. I used amber10
> package
> to calculate the parameters. The program did not recognize zinc atom
> type
> and considered as a dummy atom (DU) with zero charge and no force and
> Van
> der Waal parameters.
If you are trying to use Antechamber this will be your problem. Catalytic
metal centers are way beyond what Antechamber was ever designed to handle.
You will need to manually build your own mol2 / prep files for leap and also
provide frcmod files containing parameters that you will need to derive
unless someone has already published such parameters. I suggest starting
with the Ryde papers above and doing a citation search on these.
> Would you please help me to fix this problem? I have also attached
> Gaussian output file here.
Your first step is to do a RESP fit. I would suggest using RED as Francois
suggests. Using Antechamber will not work here. You should also take a look
in the literature regarding how such resp fits should be done when you have
zinc covalently bound to ligands. I suggest taking a look at the following:
Walker, R.C., Klug, D.R. et al. "Large and fast relaxations inside a
protein: Calculation and measurement of reorganisation energies in alcohol
dehydrogenase.", J. Phys. Chem. B., 2002, 106(46). 11658-11665
Walker, R.C., Cho, B.M., Amer, H., Mercer, I.P., Gould, I.R., Klug, D.R.,
"The effect of adiabaticity on electron dynamics in Zinc Myoglobin." J.
Phys. Chem. B., 2005, 109(12), 5954-5961
And also
http://www.rosswalker.co.uk/files/Ross_Walker_Thesis_Final.pdf
See chapter 2.
Here is an frcmod file I used for 1LDY (LADH)
Modified Parameters for 1LDY Calcs 24-12-2000
MASS
Zn 65.38
BOND
Zn-SH 81.7 2.293
Zn-NB 85.5 2.101
Zn-O 45.1 2.359
C-H2 367.2 1.080
ANGL
SH-Zn-O 31.0 104.4
SH-Zn-SH 49.5 146.5
SH-Zn-NB 30.4 103.0
CT-SH-Zn 18.9 111.6
CV-NB-Zn 44.5 123.6
NB-Zn-O 16.1 97.9
CR-NB-Zn 44.5 123.6
Zn-O-C 19.9 131.2
N-C-H2 35.0 113.2
O-C-H2 35.0 122.3
CT-CM-HA 35.0 118.0
CM-C-N 70.0 117.3
CM-CT-CM 63.0 110.2
CM-N*-CM 70.0 117.8
DIHE
SH-Zn-NB-CV 1 -2.82 0.00 2.
SH-Zn-NB-CR 1 -2.82 0.00 2.
SH-Zn-SH-CT 1 -0.03 0.00 2.
SH-Zn-O-C 1 -0.77 0.00 3.
CT-SH-Zn-NB 1 -0.03 0.00 3.
CT-SH-Zn-O 1 -0.03 0.00 3.
CV-NB-Zn-O 1 2.82 0.00 2.
NB-Zn-O-C 1 -0.77 0.00 3.
CR-NB-Zn-O 1 2.82 0.00 2.
Zn-O-C-H2 1 -1.82 0.00 2.
Zn-O-C-N 1 -1.82 0.00 2.
NONB
Zn 1.85 0.06
This has bond, angle and dihedral parameters from the Ryde papers. Adapted
for AMBER. It also has mass for Zinc - the isotopic average mass. And also
VDW params for zinc. I forget where I got these from, probably from Ryde but
check the text in my thesis to see.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Thu Jan 07 2010 - 15:30:02 PST
