Questions related to Docking
I am calculating the oniom energy for a complex, receptor only and ligand only to calculate the free binding energy of the ligand of interest. I've seen different papers that do get similar kcal/mol calculations to their respective docking experiments but wanted an opinion on if it truly makes sense to do so. Both methods are taking in completely different things when forming their calculations. I figured each would only be able to be compared relative to each other? Example. Ligands can only be compared to each other via docking alone and ligands used in oniom can only be compared to each other through oniom.
I used Cluspro to dock my protein of interest with several kinase proteins. Then, I analyzed the results using PDBsum and ProQ. I have a question regarding the ProQ results. For all my docked models, the Predicted LGscore was higher than 5, but the Predicted MaxSub was approximately -0.5. I'm not sure how to interpret this and whether I can consider my docked models acceptable or not. It's worth mentioning that I docked the entire protein, not just a short sequence, which may explain the negative value of MaxSub, is not it? Additionally, 79 to 85% of the protein residues in my models fall in the Most favored regions according to the Ramachandran Plot statistics, and the G factors range between -0.4 to -0.54. So, could someone please explain if my models are acceptable based on these statistics?
I am using PyRx as platform when I load macromolecule and ligand, the molecules get loaded. When I Dock I get this message "<PyRx.autogridPage.RunAutoGrid; proxy of <Swig Object of type 'wxPanel *' at 0xb7b94c0> >>Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26)"
Can anyone help me in resolving this issue
There is a large protein that I would dock a file containing 3 different ligands with to see if distinct binding sites are filled or not. Is any software to do so?
they are seemingly limited to one ligand docking
Thank you in advance
one of the proteins I am trying to dock has a phosphorylation at one of the residues and i want to dock it , without changing that residue, which tool can be used for such non standard, post translationally modified amino acid containing protein docking?
I'm working with a protein that does not have a co-crystallized ligand. How to analyze the best docking pose and validate the docking procedure?
Hi, after docking my drug structure gets changed( a single bond became double bond). does anyone know how to solve this problem. Thanks
I created a grid using the Autodock tools and then using those coordinates and size I created a configuration file for Vina. But in the results, the location of the ligand do not match the specified coordinates and size. I used the PyMol for visualization, but the ligand is not placed within the previously selected coordinates.
Thank you for help.
I am trying to dock a planar ligand with a receptor molecule using Autodock tool. I want to freeze the torsions of the ligand. So, I changed the number of active torsions to 0. Also, in the .dpf file I set 'torsdof' to 0. However, I'm encountering issues with this approach.
I would greatly appreciate any insights or suggestions regarding this matter.
I previously done the protein-protein docking with HEX8.0 software. But for more analysis (e.g. TMSD and s-score) of docking results, I am using the Autodock. I performed all the steps based on the Rizvi et al. (2013). When I want to write the commands in cygwins command line, I am facing with this error: "o.dpf: command not found".
Could anyone please help me by detailed steps and information?
Good morning, I'm trying to do docking with ADT for a zinc chelator having an hydroxamate group. However when I try it, the tool doesnt fit the group in the ion and I dont know why. Can anyone help me with this? I just prepare the pdb file, convert to .pdbqt and run the program..where do I mistake? Thanks anyone in advance
We need the pdb of metformin for docking studies in ClusPro.
We tried to make it from the 5G5J pdb but that pdb does not work in ClusPro. I added the pdb we made by splitting from 5G5J. Pymol can recognize it but not ClusPro.
Any recommendation would be helpful.
I was trying redock a ligand to a protein, which was already present in the PDB crystal structure. I extracted the ligand and tried to dock it again using Autodock vina in that same site specified by a grid box centered on the original position of the ligand and of size 30x30x30. The original docking mode in the crystal structure had 4 H-bonds, but the vina docking result has only one, and that too in a different position, about 10 A from the original position. I am trying it with different gridbox dimensions, with different exhaustiveness values (8, 32), but every time it is getting docked at that wrong position. It should also be noted that the docking results themselves are very consistent among themselves. (Refer to the attached image. Blue: Original position with 4 H bonds, Pink: Vina docked position with only 1 H bond)
Why is this happening? How do I get the correct docked structure? Is this a problem with vina itself, that it is not being able to find the correct docked position? If so, then is there any better tool for docking?
Hello fellow researchers,
I made a docking from one of the articles. This work was done as a practice and to ensure the correct process of doing the work. When the docking was done and I checked the result of my docking with the same article, my results were different from that article in some ways, although I must say that I had to change the settings in several steps and optimize the ligand. My question is, is the difference (although close) of the results normal and not a problem? Thanks.
I am docking small peptides up to 6 AA chain long. After so many month of trying to find a successful peptide-protein docker, i finally found Swisssdock but now the challenge is how to analyse the results. I cannot open the results in ChimeraX and pyMol which are so much farmiliar with many of us. USCF chimera I can open the results but it is difficult to create images for publications. Can I please get help with a step by step guide how to view the results from Swissdock using Discovery Studio Visualizer to analyse the interactions .
I will be greatful and highly appreate any help rendered.
I have a protein that binds to ATP and another nucleotide. I want to dock them so that I can find out the binding site residues in the protein. Which tool can I use?
I am trying to dock a ligand on PyMol using the DockingPie plugin. When I import the ligand as a pdbqt file on pymol, DockingPie gives me the option to import that ligand for docking later on. However, when I select "set ligand" in the DockingPie plugin, I receive an error stating "FileNotFoundError: [WinError 2] The system cannot find the file specified: '01_tclcactvs000ksOway_ADFR.pdbqt' -> '01_01-tclcactvs000ksOway-ADFR_ADFR.pdbqt'"
How do I go about this? Thank you!
This message is pooping up despite i am having the grid gpf file in the same folder where i am doing the docking and i have followed all the steps correctly from protein(BSA) preparation to ligand preparation(Ketoprofen). Still I am not able to run the autogrid command. While the same thing i have done for another set of protein and ligand and it worked.
Before this, I was running the docking on CB Dock just by doing the default setting which deletes all hetatoms. But after running the docking a few times, there have been suggestions to remain the hetatoms including metal ion. My question is which hetatoms need to have remained to dock and what is the important for this action. I quickly big no idea about these issues. Thank you for answering my question.
Suppose I have done docking of BSA with Ketoprofen and I have got some poses. I have selected the best suitable pose of the ligand and then I saved that complex of BSA with Ketoprofen. Now what i want to do is that I want to dock the whole complex with another ligand, i.e. now my complex is the new receptor. So if anyone knows how to do it plz tell me
Post docking I am not able to see any hydrogen bond interaction in my complex in ligplot. While when I visualised the same complex in DSV studio able to see two three conventional hydrogen bonds. Can you please help me is there any way to enhance hydrogen bonding during docking.
And is there any way to visualise the conventional H bond interaction in ligplot which were visible in DSV studio.
I would like to explain a candidate ligand (e.g, small molecule) binding to a targeted protein. As there is no comparison with other ligands, how can we explain that?
Do they have a standard cut-off for free energy binding? Or can we show H-bond interaction from the best pose of ligand and a targeted protein?
Could anyone shed some light, please?
All the best,
I am trying to perform MLSD to understand the docking interaction of 2 ligands with a receptor at a same time.
- For that I have followed AutoDock4 (10.1016/j.compbiolchem.2015.09.008 ; 10.1016/j.biochi.2018.10.007) in that "dpf" has to be generated individually and merge together
- Also I have followed AutoDock Vina (https://autodock-vina.readthedocs.io/en/latest/docking_multiple_ligands.html) with the given scripts
Successfully completed the docking in both the method but the result I obtained contains only one ligand.
Kindly help me to rectify this issues
Thanks in advance
I'm trying to dock protein with DNA. The only problem is that there is no experimental data available for my system. Based on the limited data, I did dock the system using HADDOCK. Now my concern is, it has given me 12 clusters with 4 structures in each. Can anyone tell me how to choose one structure from all the structures provided ? Also, how reliable is the docking for further processing?
I recently did docking using PyRx program, and noticed that docking multiple ligands simultaneously gives slightly different binding energy for some of the ligands compared to when each of the ligands are docked against same receptor.
Also, I observed that the interacting amino acids also differ in some ligands in the two cases.
I am studying a protein and ligand interaction using autodock4.2, I have a large dataset where I need to study around 15–20 ligands with my protein of interest I have generated 50 different conformations for each ligand using autodock 4.2. Using discover studio I have generated 2D plots, having a huge data set and low time I want to perform statistic to understand the probability of highest interacting residues.
I have attached a plot as an example, can anyone help me out, how to generate such statistics
I am having trouble with my autodock4 after creating modified docking parameter files, when i run; autodock4 -p ligand_HYDRO_protein.dpf -l ligand_HYDRO_protein.dlg
i get this errer;
autodock4: I'm sorry; I can't find or open "protein.F.map"
autodock4: FATAL ERROR: autodock4: I'm sorry; I can't find or open "protein.F.map"
What am i missing?
I am trying to dock a Ruthenium complex with a protein. As expected, Vina does not recognize Ru atom type and throws the following error:
"PDBQT parsing error: Atom type Ru is not a valid AutoDock type (atom types are case-sensitive).
> ATOM 3 RU UNL 1 0.177 1.341 0.016 0.00 0.00 +0.000 Ru"
I have tried to modify the parameters by adding the Ru parameters (with case-sensitive alternatives), however the error persists.
Please help me to rectify this error. I am not able to find any documentation on the same for Vina. I am performing the calculations on a LINUX OS.
My desired ligand only has 2d structure there is no 3d structure. So whenever I tried to get 2d interaction ligand is not a single fragment occur after docking. So I converted my 2 d structure to 3d by avogadro and then docked but it keeps on appearing. Can anyone plz help me with this how to solve it
I am facing a issue with complex visualisation in ligplot and pymol..
When I tried to open the docked PL complex in the aforementioned tools only ligands are visible and no interaction are visible...While quite satisfaction y interaction are observed when I assessed same PL file in Discovery studio . Please help me to overcome this problem
can we consider -5 kcal/mol binding energy is as good energy for small molecules like serotonin in molecular docking
I am trying to do docking in MOE. I tried protonating 100 ligands in the same order, but the system said that the size of the vector was exceeded. Do you know how I can correct this? Or what is the maximum size of the matrix to protonate?
or what is the correct procedure to prepare the ligands in MOE? :(
Can anyone please answer, how to dock the palladium complex with protein using Auto dock vina 1.5.7 software. It was showing below error while docking palladium related complexes. How to resolve this?
" Parse error on line 6 in file "C4.pdbqt": ATOM syntax incorrect: "Pd" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."
I have been trying to dock a certain protein with nd ion i downloaded from rcsb but after i add it to pyrx and try to convert it to ligand i get the following error. I tried converting the sdf file to pdb using pymol, chimeraX, avogadro, open babel but even then when i open the file it gives me this error: ligand: :UNK0:Nd and ligand: :UNK0:Nd have the same coordinates. Could someone please help?
Update: I want to dock an unbound protein with the neodymium metal ion which i downloaded from rcsb in sdf format and later tried to convert it to pdb using the aforementioned softwares for autodock to accept it but i can't get it to be accepted by autodock as a proper ligand. Apparently I am unable to get any of the rare earth elements to be accepted properly as ligands.
I want to download all the natural compounds from ZINC15 or ZINC20 database (either smi, sdf, or mol2 files).
However, directly downloading the files from the website has failed multiple times (since the files are more than 6 million).
Therefore, can anyone guide me on how to download it either via any Linux commands or any other way?
Also, if anyone has the natural compounds files already available, I would be grateful if you provide me with the same here.
Thank you for your kind consideration.
I want to do docking validation. I downloaded the protein from PDB and deleted the chains and cofactors and saved the co crystal in .pdb format from discovery studio visualizer. Subsequently, performed docking of cocrystal ligand. Then I had drawn the co crystal ligand in chem draw and energy minimized the ligand and the docked. When I open the docked conformer of both in discovery studio, the conformers merge into each other and while calculating rmsd, it shows an error - "Element types not matching the reference ligand". Kindly suggest am I going with the right method. What is the alternative?
What are the advantages of doing this, against doing just the molecular dynamics? what aditional information is the docking giving me, that the molecular dynamicsis not?
Can we perform docking the structure of two ligands? For example can we dock the structure of ZnO with the structure of any compounds of plant using Gaussian software? If we can do how to perform docking? orelse which software can we use for docking two ligands?
as the newer version of Autodock Vina 1.2 version released last year (
So I am asking for if there is any difference between these two scoring functions? And which is more reliable to conduct a new in silico research? Thank you very much.
I did docking of one ligand against seven receptor for consecutively five ligands. For each 1x1, there is 10 binding, so its 7000 time docking. Now, I have to quantify the number residue and minimum distance of each residues for this large scale data in just one script. Could someone please suggest any solution?
I tried with BINANA but there is continuous warning stated that (There is no atom named "N" in the protein residue TRP_314_X. Please use standard naming conventions for all protein residues to improve BINANA accuracy.) I attached a photo from the terminal where I ran BINANA.
Thanks in advance.
For solving chemical parameters of a single crystal, which softwares are helpful, in addition to that, which is good for doing docking analysis
I have tried this application on 2 other laptops and on 64-bit operating system, x64-based processor with 32 GB RAM,and I am facing the same issue.
I have a protein. It's binding site are not known hence I used castp for the prediction. I set the grid box in autodock vina and performed the docking with a ligand. However, when I see the docking, the ligand was not bind to its pocket where I have set the grid. Looking forward for suggestions.
I am using AutoDock 4 for covalent docking. I wonder - is it possible to provide as input a pdbqt file with multiple ligands included, and later parse the dlg output accordingly? If so - what main modifications are required to the docking process, and is there a tutorial (or examples of the format of the batched pdbqt input and output files) available? Thanks!!
If docking shows that long chain hydrocarbons have high binding affinity for a particular target protein, can this really mean that the long chain HCs will have potent inhibition in-vitro or have medicinal value since these type of compounds are usually oils and sometimes edible
A reviewer asked me to answer his question which I didn't understand exactly what he was looking for, knowing that I had calculated all the necessary docking parameters (binding h, binding energy, score, inhibition constant and interaction distances.
The question is: "In order to understand the contribution of the various interaction mechanisms, their values should be presented and discussed (how is the score function composed?)". Is there anyone who can help me understand his question?
Hi, guys. I started doing some dockings a few days ago and there was an constantly error showing up on the autodocktools cmd:
"swig/python detected a memory leak of type 'BHtree *', no destructor found." (PFA a printscreen of the error).
The error kept showing up after every command i gave. For example, after every missing atom added it showed up again. I didn't mind at first, because everything was working just fine, even though I was wondering if my results would be realiable with such an error.
But now, there is another error showing up on the autodock (You can also find a printscreen attached), and i can't dock anything anymore. I have already tried reinstalling autodock and MGLtools.
Has anyone had this same errors? Would you know how can I solve it? Just making clear that I'm not familiar with programming.
Thank you so much!
I have just started antibody-antigen docking and previously understood that protein-ligand docking needs to be validated using redocking. But, does redocking also apply to validating antibody-antigen docking? Thanks for your sharing about this
Hi all, I am trying to coordinate zinc to the NMR structure PDB ID: 1sp1 (a C2H2 zinc-finger) using HADDOCK. To make it clear, the PDB structure is zinc coordinated, and I am using it as a system to learn and troubleshoot some issues I am having in HADDOCK.
Briefly, (1) zinc is removed from the NMR structure (1sp1) to generate the protein input file (Chain A), (2) protein is removed from 1sp1 to generate the zinc ion input file (Chain number was changed to D (Chain D)).
Inputting both files to HADDOCK has no error.
Everything on the HADDOCK server was set to default except inputting the unambiguous restrain file (file name: test.tbl; please see the file contents below).
assign (segid A and resid 5 and name SG) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 8 and name SG) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 21 and name NE2) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 25 and name NE2) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
HADDOCK generated clusters within ~12 hours, but the zinc ion is >10 nm away from the protein coordination site. Please see the link below with all the input data I used to generate a complex.
I would appreciate it if someone guides me in troubleshooting what is wrong I am doing here or if I am missing something that I need to input.
HADDOCK results are accessible (see the link below)for your reference
I have completed virtual screening of around 3 thousand drugs from bindingdb database using PyRx software. But in the docking result there are some drugs with no proper ID. As a result I couldnt find the structure and other information. Is there any way to find out the ID using uff?
i put the pdbqt files into autodock 1.5.7 to check the rmsd value. but one does not shows up and the other has a high value for model 1 even though its position more or less the same as model 2. Thank you in advance also i docked using vina if that helps.
Can anyone give a brief explanation about the relationship between ligand size (specifically, ligands smaller than 200 MW) and binding affinity in the in silico docking?
With the increasing of MW, can there be more false positives?
Really appreciate if you can give an idea about above matter or suggest a paper that deals with above issue...
Can somebody assist me in fixing this issue produced during the preparation of macromolecules via the Python molecular viewer for docking by Wbina?
ERROR: The PDBQT file cannot be created because all atoms do not have an autodock_element field.
How can I dock more than one protein with more than one ligand, I know that pyrx is the software which docks 1 protein with multiple ligand but how can I do it for multiple proteins with multiple ligands?
what are the alternate servers for PRODRG to generate ligand topology? I have tried ATB, ACPYPE also but ligand gets detached from the protein while generation complex.gro file in the MD run. Kindly suggest!!
Thanks in advance