you have add parameter for Ni in. GPF file.

Have a look at below link for guidance.

http://mgldev.scripps.edu/pipermail/autodock/2009-March/005439.html

HTH

To further clarify Shafi Ullah Khan answer, here is a brief explanation regarding to addition of new atom parameters to AutoDock: http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock

Basically, the steps you need to do before running AutoGrid:

Hope these helps and all the best!

Nor Farrah Wahidah Ridzwan thank you,,,,.. i will try this....

Adina Kazmi Thank you for the question. I am trying to find out the solution for this as well.

Nor Farrah Wahidah Ridzwan Thank for your descriptive answer.

By the way, I believe the autodock website is down at this time am I correct? I have not been able to access it for days. http://autodock.scripps.edu/

Jakkapon Phanthuwongpakdee Good Luck

Go through this...

http://mgldev.scripps.edu/pipermail/autodock/2009-March/005439.html

Shefin Basheera Hi... Do you by any chance got the step of adding new atom described in this link? http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock The site is not accessible and I tried searching from the pipermail... still no luck... Thank you!

Jakkapon Phanthuwongpakdee .. U r right..... the website seems temporarily unavailable now. first time im noticing like this.

Shefin Basheera Okay... that is unfortunate. I thought it is only me who cannot access it. Anyway, I will ask around if someone happen to save the procedure in his/her computer. Thank you!

Dear Jakkapon Phanthuwongpakdee , here is the link to AutoDock and AutoDockTools: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/

If you are using linux, do inform me as I have those as well. All the best.

[Update]

The autodock site is now fully functional so I'd close the link. Thanks

Please refer to here.

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

Nor Farrah Wahidah Ridzwan Thank you very much. Do you any chance have the instruction on how to add new atom parameters? I believe we will also need to download .dat file, which is no longer available in the website since the website is down. Again, thank you!

Farzan Nabati As I said the site is no longer accessible but thank you.

Jakkapon Phanthuwongpakdee , the instructions are as described previously. The original .dat file should be available within the autodock folders. Do have a look and just edit it accordingly and save it with a new name.

Nor Farrah Wahidah Ridzwan Thank you! I will try as per your recommendation.

The parameters for heteroatoms are as mentioned below,

Copy the parameter you want in to the AD4_parameter.dat file. (line 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

Harinadu rajaprakash thank you , your answer helped me clearly

Hello my name is Sophie and and I am docking metal ligands to DNA. Unfortunately I have two problems. Firstly I put the parameters of Ruthenium in .dat file, although grid is running, the docking isn't. Lastly I cannot find a tutorial about docking metal complexes with DNA. Thank you very much

@Sophie Balou if you are working with metal complex you also need to add parameter into the bound.dat file.Adding in parameter. dat are meant for receptor or protein having metal ions.

Regarding the tutorial

you can use same protocol for protein-ligand one. Just

Treat DNA as protein.

Hope it will work fine.

Harindu Rajapaksha

Your answer helped me a lot!

I would like to ask you where I can find the .gpf and .dpf file has this step is blocking me completely.

Thank you in advance!

Adriano Chessa These files can be found in your working directory.

please how we can enter copper parameter in .gpf and .dpf files? Where we can find AD4-parameters.dat????

Hi Hasnia Abdeldjebar ,

Please read the previous answers and discussion on this thread since it does provide the solution/answers you are looking for.

Nonetheless, if it is not clear to you, do provide us with more specific questions so that we can assist you accordingly.

hi, Nor Farrah Wahidah Ridzwan ,

I added the copper parameters in the AD4-Parameters.dat (# Copperatom_par Cu 3.50 0.005 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding ), but I can’t always dock my complex with the receptor. the program shows me the same mistake

: \autogrid4.exe: ERROR: unknown ligand atom type Cu add parameters for it to the parameter library first!

hi Harindu Rajapaksha ,

I added the copper parameters in the AD4-Parameters.dat (# Copperatom_par Cu 3.50 0.005 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding ), but I can’t always dock my complex with the receptor. the program shows me the same mistake

: \autogrid4.exe: ERROR: unknown ligand atom type Cu add parameters for it to the parameter library first!

Hasnia Abdeldjebar

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

please aline each segment with their correpeonding colume.

Harindu Rajapaksha ,please am facing the same problem. Can you help me out on how to solve the problem encountered

How can I do with this mistake (such as follow)?

autogrid4: ERROR: unknown ligand atom type Se

add parameters for it to the parameter library first!

Hi,

I think, the question is still relevant. I recommend a video:

https://www.youtube.com/watch?v=ktJBrjlcgZc

Hello all, I have added parameters of Nickel atom in dat file. But still binding affinity values are showing +60 kcal/mol.

Any suggestion or inputs please?? Thank you

Does any one has the AD4.1_bound.dat files for Ag and B?

Bandita Datta please follow this thread https://www.researchgate.net/post/How-can-I-parametrize-an-atom-for-Autodock-Tools

to get parameters for Ag or another atom

Can anyone provide the reference paper of the atomic parameters mentioned by Harindu Rajapaksha in his post?

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