Can you please elaborate what did you mean by you can't add? What kind of operating system are you using? Is it a Window's problem you are talking about? Or can't you find it on your computer?

AD4_parameters.dat is a simple text file. You can edit it using any text editor such as gedit or even notepad in windows. You should be able to add anything to it and delete anything from it.

Please see the Autodock documentation on how to add parameters:

http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock

I am using Windows operating system. My ligand has Cobalt atom. so I tried to add atomic parameter file for Cobalt atom in AD4_parameters.dat file. but i can't add.

I still don't understand what's preventing you? Whatever.

Open the AD4_parameters.dat file with Notepad and append the following line at the end of the file:

atom_par Co 2.87 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

Then save the file and close Notepad. It is that simple.

It is deceptively simple to add parameters for a new atom in Autodock. However, when you do this, please bear in mind the caveats, as described in the link below:

http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4

Moreover, although the following pertains to molecular dynamics simulations, similar caveats apply when altering force field parameters:

http://www.gromacs.org/Documentation/How-tos/Parameterization

Thank you very much  to Rudy J Richardson and Uttam Pal. Now i got it.

Sir,  I am still facing same problem even after adding the Cobalt parameters in AD4_parameters.dat , when I run the docking programme it says Unknown atom type Co, that means parameter are missing ??

Same error I am facing with the Cr atom. Please tell me where to add the parameter. is it in the gpf file or dpf one? The steps mentioned in the autodock link above are to be followed. Am I right? 

solution:

Open the AD4_parameters.dat file with Notepad and append the following line at the end of the file:

atom_par Co 2.87 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

Then save the file and close Notepad. It is that simple.

For more information:

It is deceptively simple to add parameters for a new atom in Autodock. However, when you do this, please bear in mind the caveats, as described in the link below:

http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4

Moreover, although the following pertains to molecular dynamics simulations, similar caveats apply when altering force field parameters:

http://www.gromacs.org/Documentation/How-tos/Parameterization

This is what I am trying but how will I get the values for chromium? Since i am a beginner, i need to understand. These values specifically include:

van der Waals radius of the atom/ion (in Angstrom); specify twice this value in the "Rii" field

epsilon or energy well depth for two like interacting atoms/ions (in Kcal/mol); specify in the "epsii" field

volume of the atom/ion (in Angstrom^3); compute this from 4/3 * PI * (Rii/2)^3; specify in the "vol" field

atomic solvation parameter of the atom/ion; the ai or "ASP" values in the equation for Si in the description of the Desolvation Free Energy Term in AutoDock 4; specify this in the "solpar" field

How to get these?

Sorry.In my case, there is no Cr atom. i don't know where you will get parameters of Cr atom. My suggestion is better you can do QM/MM study.

okay thank you

@ Uttam Pal when the AD4_parameter file was opened using notepad, it opened as a txt file. Please after adding features for the required atom (parametizing) which file did you save it as

Irrespective of the file name extensions, it is basically a text file. In the windows folder option unselect "Hide file type extensions for known file types". Then windows will show you the extensions such as .txt or .text or .dat.txt or whatever. You can change it using rename option.

@ Uttam Pal thank you for your prompt response. I tried but it kept telling me error that it is opened in notepad++. If I try to force/bypass if to save the following messages appear: (1) you don't have permission to save in this location; (2) contact administrator to obtain permission; (3) would you like to save in the My Documents folder instead.

Save in the My Documents, then. You can also specify parameter file names in .gpf and .dpf files.

Thanks a lot to all of you for this valuable and fruitful discussion.

Suvendu Paul.

Hi, I need for the Chromium atomic parameter

@Uttam Pal sir after saving the file, how to run the command of .gpf and .dpf files. ??

@Adina Kazmi, just include the file while preparing .gpf and .dpf. See the attached animated .gif file.

Uttam Pal thank you sir for guidance,,,.. but i am stuck with this issue now kindly help

Hello Guy, is there any other database I can find atomic parameters for Mg 2+ and Mn 2+ ion please other than the ones listed on Autodock web page.

The parameters for heteroatoms are as mentioned below,

Copy the parameter you want in to the AD4_parameter.dat file. (align rows the values to the correct rows)

Then you need to past the modified bat file to the folder were the autodock and autogrid exe file are.

The you need to modify the .gpf and .dpf file by adding "parameter_file AD4_parameters.dat" command. then you are good to go.

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 4 # Non H-bonding

atom_par Li 2.45 0.025 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Be 2.76 0.085 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par B 4.08 0.180 12.052 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ne 3.24 0.042 15.440 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Na 3.98 0.030 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Al 4.49 0.505 11.278 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Si 4.30 0.402 12.175 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par K 3.81 0.035 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sc 3.30 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ti 3.18 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # 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 4 # Non H-bonding

atom_par Ni 2.83 0.015 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cu 3.50 0.005 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ga 4.38 0.415 11.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ge 4.28 0.379 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par As 4.23 0.309 13.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Se 4.21 0.291 14.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Kr 4.14 0.220 16.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Rb 4.11 0.040 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sr 3.64 0.235 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Y 3.35 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Zr 3.12 0.069 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Nb 3.17 0.059 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Mo 3.05 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tc 3.00 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ru 2.96 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Rh 2.93 0.053 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pd 1.34 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cd 2.85 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par In 4.46 0.599 11.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sn 4.39 0.567 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sb 4.42 0.449 13.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Te 4.47 0.398 14.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Xe 4.40 0.332 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cs 4.52 0.045 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ba 3.70 0.364 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par La 3.52 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ce 3.56 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pr 3.61 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Nd 3.58 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pm 3.55 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sm 3.52 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Eu 3.49 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Gd 3.37 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tb 3.45 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Dy 3.43 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ho 3.41 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Er 3.39 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tm 3.37 0.006 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Yb 3.36 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 1 4 # Non H-bonding

atom_par Lu 3.64 0.041 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Hf 3.41 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ta 3.71 0.081 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par W 3.07 0.067 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Re 2.95 0.066 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Os 3.12 0.120 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ir 2.84 0.073 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pt 2.75 0.080 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Au 3.29 0.039 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Hg 2.71 0.385 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tl 4.35 0.680 11.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pb 4.30 0.663 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Bi 4.37 0.518 13.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Po 4.71 0.325 14.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par At 4.75 0.284 15.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Rn 4.77 0.248 16.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Fr 4.90 0.050 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ra 3.68 0.404 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ac 3.48 0.033 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Th 3.40 0.026 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pa 3.42 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par U 3.40 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Np 3.42 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pu 3.42 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Am 3.38 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cm 3.33 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Bk 3.34 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cf 3.31 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par E 3.30 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Fm 3.29 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

You can't directly dock a metal or metal containing ligand using autodock. First you need to incorporate the parameters.

Follow this:

http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Scientific%20Questions

I have modified the AD4 parameter but couldn't find .dpf and .gpf files.

I have edited the Autodock parameter tool file, but I faced an error also,

Could have anybody guidance for me in this way?

Harindu Rajapaksha Thank you very much for the parameter table!

What is the source and/or reference for the values?

Eugene V. Radchenko https://autodock.scripps.edu/how-to-add-new-atom-types-to-the-autodock-force-field/ provides the link to the parameter table which is found here:

https://autodock.scripps.edu/wp-content/uploads/sites/31/2019/03/AD4.1_bound.dat

To add Cobalt atomic parameter in Autodock 4.2, you can modify the force field parameter files (*.dat) to include the Co atom type and its parameters.