ADL: Parameters for docking with metal ions in receptor

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

ADL: Parameters for docking with metal ions in receptor

DimitryASuplatov
Hello,
I was concerned about using copper and sodium cations with autodock 4.
Since none of those are in the default ff file, I did a little search
in the internet. Finally I can give you this batch (see below). I`ve
tested it for Cu and Na and did not observe any severe errors.

The idea of this message is to
1/ Give starting parameters for those who want to run a docking
experiment from scratch
2/ Start a thread discussing this parameters. May be some of you have
something better that you would like to share. It shall also be
appreciated to discuss possible errors.

SDA

# $Id: AD4_parameters.dat,v 1.4 2005/10/31 18:36:45 rhuey Exp $
# AutoDock Parameters - Version 1.0

#
# AutoDock 4 coefficient with respect to original (AD2) parameters
#

FE_coeff_vdW 0.1560
FE_coeff_hbond 0.0974
FE_coeff_estat 0.1465
FE_coeff_desolv 0.1159
FE_coeff_tors 0.2744

# - Unweighted vdW and Unweighted hbond Well Depths
#
# - To obtain the Rij value for non H-bonding atoms, calculate the
# arithmetic mean of the Rii values for the two atom types.
#
# - To obtain the epsij value for non H-bonding atoms, calculate the
# geometric mean of the epsii values for the two atom types.
#
# - Note that the Rij_hb value is non-zero for heteroatoms only, and
zero for H atoms;
# to obtain the Rij_hb for an H-bond, look up for the heteroatom only;
# do not combine Rij_hb values between heteroatoms and hydrogens;
# Similarly, for epsij_hb values.
#
# For example, the Rij_hb for OA-HD H-bonds will be 1.9 Angstrom,
# and epsij_hb will be 5.0 kcal/mol .
#
# Rii Rij_hb rec_index
# Atom epsii solpar epsij_hb map_index
# Type vol hbond bond_index
# -- ---- ----- ------- -------- --- --- - -- -- --
atom_par C 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par A 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par N 3.50 0.160 22.4493 -0.00162 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par NA 3.50 0.160 22.4493 -0.00162 1.9 5.0 4 -1 -1 1 # Acceptor 1 H-bond
atom_par NS 3.50 0.160 22.4493 -0.00162 1.9 5.0 3 -1 -1 1 # Acceptor S Spherical
atom_par OA 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor 2 H-bonds
atom_par OS 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor S Spherical
atom_par SA 4.00 0.200 33.5103 -0.00214 2.5 1.0 5 -1 -1 6 # Acceptor 2 H-bonds
atom_par S 4.00 0.200 33.5103 -0.00214 0.0 0.0 0 -1 -1 6 # Non H-bonding
atom_par H 2.00 0.020 0.0000 0.00051 0.0 0.0 0 -1 -1 3 # Non H-bonding
atom_par HD 2.00 0.020 0.0000 0.00051 0.0 0.0 2 -1 -1 3 # Donor 1 H-bond
atom_par HS 2.00 0.020 0.0000 0.00051 0.0 0.0 1 -1 -1 3 # Donor S Spherical
atom_par P 4.20 0.200 38.7924 -0.00110 0.0 0.0 0 -1 -1 5 # Non H-bonding
atom_par Br 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par BR 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Cl 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par CL 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par F 3.09 0.080 15.4480 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par Fe 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par FE 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par I 4.72 0.550 55.0585 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par Mg 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par MG 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Mn 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par MN 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par ZN 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par He 2.36 0.056 15.240 -0.00110 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par Li 2.45 0.025 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Be 2.76 0.085 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par B 4.08 0.180 12.052 -0.00110 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par Ne 3.24 0.042 15.440 -0.00110 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par Na 3.98 0.030 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Al 4.49 0.505 11.278 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Si 4.30 0.402 12.175 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par K 3.81 0.035 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sc 3.30 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ti 3.18 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par V 3.14 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Co 2.87 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ni 2.83 0.015 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cu 3.50 0.005 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ga 4.38 0.415 11.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ge 4.28 0.379 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par As 4.23 0.309 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Se 4.21 0.291 14.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Kr 4.14 0.220 16.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Rb 4.11 0.040 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Sr 3.64 0.235 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Y 3.35 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Zr 3.12 0.069 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Nb 3.17 0.059 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Mo 3.05 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tc 3.00 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ru 2.96 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Rh 2.93 0.053 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pd 1.34 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cd 2.85 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par In 4.46 0.599 11.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sn 4.39 0.567 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sb 4.42 0.449 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Te 4.47 0.398 14.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Xe 4.40 0.332 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cs 4.52 0.045 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Ba 3.70 0.364 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par La 3.52 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ce 3.56 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pr 3.61 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Nd 3.58 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pm 3.55 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sm 3.52 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Eu 3.49 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Gd 3.37 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tb 3.45 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Dy 3.43 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ho 3.41 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Er 3.39 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tm 3.37 0.006 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Yb 3.36 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Lu 3.64 0.041 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Hf 3.41 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ta 3.71 0.081 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par W 3.07 0.067 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Re 2.95 0.066 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Os 3.12 0.120 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ir 2.84 0.073 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pt 2.75 0.080 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Au 3.29 0.039 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Hg 2.71 0.385 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tl 4.35 0.680 11.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pb 4.30 0.663 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Bi 4.37 0.518 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Po 4.71 0.325 14.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par At 4.75 0.284 15.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Rn 4.77 0.248 16.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Fr 4.90 0.050 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Ra 3.68 0.404 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Ac 3.48 0.033 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Th 3.40 0.026 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pa 3.42 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par U 3.40 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Np 3.42 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pu 3.42 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Am 3.38 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cm 3.33 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Bk 3.34 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cf 3.31 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par E 3.30 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Fm 3.29 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: Parameters for docking with metal ions in receptor

dr. sakura
Hello, I'm not an expert on parameters, so don't know if what you've found
out works, but have to remind you -since I came across the same issue-
XCSCORE scoring function cannot distinguish different metals.

Take a look at this thread:
http://autodock.1369657.n2.nabble.com/ADL-Heme-groups-td7579604.html#a7579618


Good luck,



--
Sent from: http://autodock.1369657.n2.nabble.com/
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---