Dear  Pallab Kumar Borah,

First you finished your docking after u save as pdb file. After you used PYMOL virtual tool you opened the pdb file its will come automatically Mr. Pallab Kumar Borah. Any doubt ask me.

Thank you for the reply. But, I have a ligand database of about 200 ligands. I need to check them against a receptor. How do I program Vina to run them respectively one after the other, without having to manually write a config file seperately for each ligand to be docked. Any specific commands available in the command line interface ??

Scripting is a good option, but did you try pyrx for autodockvina.

Dr. Vetrivel, yea scripting. But m not very familiar with scripting and havent found any helpful tutorial online.

try pyrx its Gui tool

Pyrx also not possible. I tried Sir Dr.Umashankar Vetrivel

Dear Pallab Kumar Borah!

Youtube tutorials are HELPful to learn AutoDock program. Please visit the following youtube link.

https://www.youtube.com/results?search_query=autodock

First learn AutoDock, then only you can able to understand the AutoDock Vina easly. Please find the AutoDock Vina snapshots and model config.txt file for Vina.

Now, AutoDock Vina plug-in is available on PyMOL

http://wwwuser.gwdg.de/~dseelig/adplugin.html

I hope you remember, Linux environment is better to work with AutoDock/Vina.

I hope this will HELP you

ALL THE BEST

----

Check the bioactivity the ligands using Online Server

http://www.pharmaexpert.ru/passonline/

Optimize the ligand before you docking

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/submit.html

Dear D. Mani Maran, thank you very much for the response. The suggestions were really helpful. Thank you. Have a great day.

I finally figured out a working solution to this problem..... If anybody would like to know.... please inbox me in RG

Hello Pallab, I am having the same problem. Have you find a way to program the loop to screen several .pdbqt files? 

Hello Pallab,

Kindly find the tutorial link to separate the best conformer from the final.pdbqt file for generating the binding pose figure.

https://www.youtube.com/watch?v=DiF7LxHrmSo

Hope it's HELP :-)

Thank a lot Dr. Mani

Dear Dr. Candelaria... I finally compiled a shell script to do the job.... If you need any help please inbox me

I am able to use vina for docking a single ligand but I have to screen a library of ligands on a protein receptor and don't know how to do it through vina.

Tutorials available online aren't very helpful. I tried to download Pymol plugin for vina but it doesn't open on my laptop which has a Windows 7 OS. I would appreciate any help on this topic. Thanks

Dear Pallab Kumar Borah,

I'm also stuck with the same problem... I need to dock almost 500 compounds, any advice?

Thanks in advance

The script that I use should do your job. But, 500 ligands will make the script insanely long. You may attempt to modify the script. I can send you the procedure.

I am so sorry to not being able to reply individually,

U may use this script....

#! /bin/bash

for f in ligand_*.pdbqt; do

b=`basename $f .pdbqt`

echo Processing ligand $b

mkdir -p $b

vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt

done

Dear Pallab,

Thank you for sharing. Please what is the command for the execution on window 7

Dear Asmau,

It's good with Linux. But if you plan to use it on a windows machine, Cygwin is your friend. I have also run them on the cmd before.

Dear Pallab,

Thank you for your response. Although am not clear with it.

Dear Asmau,

U can use this code as a .sh file, and run it in Cygwin (if you are using Windows, as ./some_name.sh). Cygwin provides a Linux like environment on Windows machines. All you ligand files, protein files, config file, and this .sh code, should exist on the same directory (folder) for the code to run properly.

Happy Docking...

Hello Pallab,

This is the error am getting;

./VS.bash: line 2: ./Vina/vina: No such file or directory

grep: *.txt: No such file or directory

The folder contains all the lig.pdbqt ,rec.pdbqt, vina folder,VS.bash file, conf.txt

Attached is my VS.bash

The execution command i used; is ( ./VS.bash)

Thank you for your assistance

Asmau Hamza

Usually, all .sh run under bash compatibility, but all bash cannot run under .sh.

This might be silly, but try saving as a .sh file....

Hi Asmau Hamza,

I hope Dr. Pallab Kumar Borah's suggestions are HELPful for you. If you trying this calculations in Windows platform. I request you to add 'vina.exe' instead of 'vina'

vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt

changed into

vina.exe --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt

Avoid uppercase letters. Space character are case sensitive. Review at once your 'conf.txt' file. Let me know, it is HELPful

Thanking you

---

with kind regards,

Mani

 Mr Pallab kumar, Helo

i wish to help me for virtual screening using autodock in Mac OS x

the tutorial does 'nt help me

Dear Rahal, I do not have any experience with the Mac OS. Sorry

First and foremost I would like thank to all who contributed to this discussion especially Mr. Pallab Kumar Borah who initiated it.

I am also a 'newbie' with autodock, autodocktools and vina therefore this discussion helps me a lot.

After several failure attempts, I finally manage to get it working on Windows 10.

Here I would like to share some of the key features that I wish I knew earlier:

1) Install Cygwin (https://cygwin.com/install.html) and configure it in Windows Environment

- follow the instructions provided here: https://www.maketecheasier.com/install-configure-cygwin-windows/

2) Using the similar instruction as above, set a path for vina in Windows Environment as well

3) Make sure the scripts are editted properly according to your file name

•  "for f in ligand_*.pdbqt; do"

- "ligand_*" more or less stands for your ligands name file (ligand_1, ligand_42, ligand_342, etc.)

- therefore feel free to change it according to your own ligands file name

•  "vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt"

- "vina" is the 'path' to the vina application installed on your system

- identifying the location and editting this part is essential

- example: C:/Vina/vina.exe --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt

Hope these help!

@Farrah Wahidah Ridzwan : Thank you very much for your answer sir. It helped me a lot.

#! /bin/bash for f in *.pdbqt; do b=`basename $f .pdbqt` echo Processing ligand $b mkdir -p $b vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt done

We have developed a pipeline for ligand preparation to virtual screening called poap ..published in computational biology and chemistry. ..i guess will be useful. https://doi.org/10.1016/j.compbiolchem.2018.02.012

hi all... im getting an error. when i tried to do virtual screening using cygwin. this is the error im getting.. somebody plz help. Sorry to say im new to scripting.

Dell@Dell-Pc /cygdrive/d/The Scripps Research Institute/vina

$ ./vs.sh

./vs.sh: line 2: $'\r': command not found

./vs.sh: line 3: syntax error near unexpected token `$'do\r''

'/vs.sh: line 3: `for f in ligand_*.pdbqt; do

kindly help me to resolve this.

Shefin

Hi! I am trying to perform a virtual screening with autodock/vina for in sillico saturation mutagenesis. So, in this case I have a library of about 200 different proteins all with the same coordinates and one single substrate.

Can this be done with a script? How can I make it work with several different receptors and one ligand.

Hope you can help me or point me in the right direction.

Best regards,

Enrique Ordaz

We have developed a pipeline for ligand preparation to virtual screening called poap ..published in computational biology and chemistry. ..i guess will be useful. https://doi.org/10.1016/j.compbiolchem.2018.02.012

In poap u hv option for multiple receptor vs. Single ligand..try it..if u have any queries feel free to contact me

I have 15 different ligands and 1 receptor protein. I have successfully completed my docking with autodock vina .Now i am facing problem in interpreting my results for comparative anlaysis. So Can anyone pls help me how to study comparative analysis between different protein-ligand complexes using auto dock Vina. ?

Thank You.

... and if you happen to stumble upon syntax error near unexpected token `$'do\r'' and/or -bash: '\r': command not found message(s) after you try to run your script, don't panic and just open your .sh file in Notepad++ and press CtrlH and replace all [\r\n]+ with \n

Also, if you get vina: command not found error, just add ./ before vina, so

./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt

If you keep having problems try also to copy/paste your vina.exe into your working folder.

Also, for total n00bz like me: you run your script file (ie script.sh) with bash script.sh

Just my 2 cents.

Milos Svircev Hi, I'm using autodock vina in an HPC, but can't figure out how to utilise more CPUs as I have an entire database to screen against my protein. How you be kind enough to help me with this?

I tried this script...it works nicely but too muchhhhhh slow... I just used it for 2568 ligands in an ubantu 18.04 system running over i9 10core processor with 2 gpu containing 3k scudamore each....lol it takes only one processor and no gpu ...almost takes 37hrs to complete...

now encountered by new problem ...

that program generated 2568 folders containing output files with 8 to 9 docking pose....it's a big challenge for me now how will I check all of them to get the best molecule with satisfactory properties.... any script for analysis??? or any idea

Yes, there is one script called

topmolecule.py

Sadly, the code isn't magically parallel. So it will be great if someone can contribute to the magic.

Mursaleen Baba I'm afraid I can't help you right now, as I don't know the answer. But that's definitely something worth googling for. What I do when I'm overwhelmed with ligands, though, is "divide and conquer" approach: I distribute ligands to several computers. So the fastest machine gets most ligands to chew on etc. you get the idea.

It's convenient if all machines have some remote desktop app installed so I can monitor/control the whole process.

Create a .txt script and copy this:

#! /bin/bash

for f in Ligand*; do

a=`basename $f`

cp /home/MyUserName/job/conf.txt /home/MyUserName/job/$a

cp /home/MyUserName/job/protein_rigid.pdbqt /home/MyUserName/job/$a

cp /home/MyUserName/job/protein_flex.pdbqt /home/MyUserName/job/$a

t=/home/MyUserName/job/VS_Results.txt

cd $a

for g in ZINC*.pdbqt; do

b=`basename $g .pdbqt`

echo Processing ligand $b

mkdir -p $b

vina --config conf.txt --ligand $g --out ${b}/out.pdbqt --log ${b}/log.txt

vina_split --input ${b}/out.pdbqt

cd $b

awk 'NR>=27 && NR

Muniba Faiza

I run the vina_vs.sh from the link you posted. There is something wrong with it. See attached. Any suggestions?Thanks.

@Arun Kumar Jaiswal - Can you be little more specific with the command script.