-filelist execution

[debanjansen48]

thank you for the update. But i am unable to run batch operation please help me out.

in the working directory i put my protein information including map.fld file in a folder name protein and all ligands in pdbqt for mat in a folder lig then issued the command given bellow

/ADT-Gpu/batch$ ./autodock_gpu_256wi -ffile ./protein/ -filelist ./lig

Error: ligand pdbqt file was not defined. Use -lfile argument!

how to resolve.

[L30nardoSV]

Hi @debanjansen48,

First, the arguments for -ffile and -filelist are files, not folders, as you specified above.

Second, please follow the format guidelines suggested here: https://github.com/ccsb-scripps/AutoDock-GPU#supported-arguments

Basically, for the -filelist <MYFILE> option you need to specify a <MYFILE> with this format:

./receptor1.maps.fld
./ligand1.pdbqt
Ligand 1
./receptor2.maps.fld
./ligand2.pdbqt
Ligand 2
./receptor3.maps.fld
./ligand3.pdbqt
Ligand 3

[debanjansen48]

respected sir

As I understood I have to write a command (as per you mentioned)

in terminal $ ./autodock_gpu_256wi ./receptor1.maps.fld ./ligand1.pdbqt Ligand 1 ./receptor2.maps.fld ..........

and so on for 1 million ligands?

you mentioned receptor1 receptor 2 etc.... but I have only 1 receptor and 1million pdbqt file...

Plz help

On Sat, Jun 20, 2020 at 7:20 PM Leonardo Solis V. notifications@github.com wrote:

Hi @debanjansen48 https://github.com/debanjansen48,

First, the arguments for -ffile and -filelist are files, not folders, as you specified above.

Second, please follow the format guidelines suggested here: https://github.com/ccsb-scripps/AutoDock-GPU#supported-arguments

Basically, for the -filelist option you need to specify a

with this format: ./receptor1.maps.fld ./ligand1.pdbqt Ligand 1 ./receptor2.maps.fld ./ligand2.pdbqt Ligand 2 ./receptor3.maps.fld ./ligand3.pdbqt Ligand 3 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or unsubscribe .

[L30nardoSV]

Hi @debanjansen48,

No, basically you have to create a file (e.g., MYFILE) were you add the list of receptors, ligands and name for the output of each docking. Using this file, you do not have to specify the molecules within the command.

If you have a single receptor and many ligands, the contents of your MYFILE can be like this:

./receptor.maps.fld
./ligand1.pdbqt
Ligand 1
./ligand2.pdbqt
Ligand 2
...
<more ligands and names for the .dlg files>
...

Then, you can run that with this command:

$  ./autodock_gpu_256wi -filelist MYFILE <other options>

<other options> can be:

• -nrun, -lsmet, etc
• but not -ffile, -lfile (as molecules are already specified in MYFILE)

Hope this helps!

[debanjansen48]

i prepared MYFILE (list_lig.txt) as follows

---

./6lu7.maps.fld ./NPC1486.pdbqt Ligand 1 ./NPC1704.pdbqt Ligand 2 ./NPC1744.pdbqt Ligand 3 ./NPC1811.pdbqt Ligand 4 ./NPC1886.pdbqt Ligand 5 ./NPC1991.pdbqt Ligand 6

---

then issued the command autodock_gpu_256wi -filelist list_lig.txt -nrun 5 -lsmet

(the directory possess the file 6lu7.maps.fld)

but it returns Error: grid fld file was not defined. Use -ffile argument!

"(base) dLab@deb:~/Desktop/ADT-Gpu/batch/ligs$ autodock_gpu_256wi -filelist list_lig.txt -nrun 5 -lsmetError: grid fld file was not defined. Use -ffile argument!"

On Mon, Jun 22, 2020 at 12:53 PM Leonardo Solis V. notifications@github.com wrote:

Hi @debanjansen48 https://github.com/debanjansen48,

No, basically you have to create a file (e.g., MYFILE) were you add the list of receptors, ligands and name for the output of each docking. Using this file, you do not have to specify the molecules within the command.

If you have a single receptor and many ligands, the contents of your MYFILE can be like this:

./receptor.maps.fld ./ligand1.pdbqt Ligand 1 ./ligand2.pdbqt Ligand 2 ... <more ligands and names for the .dlg files> ...

Then, you can run that with this command:

$ ./autodock_gpu_256wi -filelist MYFILE

can be: - -nrun, -lsmet, etc - but not -ffile, -lfile (as molecules are already specified in MYFILE) Hope this helps! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or unsubscribe .

[diogomart]

@debanjansen48 did you compile AutoDock-GPU yourself? If you are using the precompiled binaries that explains the problem, because they were compiled before the -filelist feature was implemented.

[debanjansen48]

I compiled before as per the instruction " https://github.com/ccsb-scripps/AutoDock-GPU/issues/80#issuecomment-629980303 "

That works nicely for me during single ligand docking

On Wed, Oct 28, 2020 at 10:15 PM Diogo notifications@github.com wrote:

@debanjansen48 https://github.com/debanjansen48 did you compile AutoDock-GPU yourself? If you are using the precompiled binaries that explains the problem, because they were compiled before the -filelist feature was implemented.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ccsb-scripps/AutoDock-GPU/issues/89#issuecomment-718063847, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4U7NUN6GUB5ZSH354LSNBDDVANCNFSM4ODMM4PQ .

[debanjansen48]

yes....I newly compiled it as per the previous instructions. and used the command

./autodock_gpu_256wi -filelist lig_list.txt

it works... Thanks.. thanks... I want to know is it necessary to put "./" before every ligand and Ligand 1 or 2 etc after every line

Actually i created the list by

ls >> lig_list.txt

then in the lig_list.txt file manually i put "./"

sorry to say I am not a linux expert.... in order to discover "ls >> lig_list.txt" i just consumes huze time.. that is why asking you sir. is there any other way to make it easy..

On Wed, Oct 28, 2020 at 11:35 PM Debanjan Sen debanjansen48@gmail.com wrote:

I compiled before as per the instruction " https://github.com/ccsb-scripps/AutoDock-GPU/issues/80#issuecomment-629980303 "

That works nicely for me during single ligand docking

On Wed, Oct 28, 2020 at 10:15 PM Diogo notifications@github.com wrote:

@debanjansen48 https://github.com/debanjansen48 did you compile AutoDock-GPU yourself? If you are using the precompiled binaries that explains the problem, because they were compiled before the -filelist feature was implemented.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ccsb-scripps/AutoDock-GPU/issues/89#issuecomment-718063847, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4U7NUN6GUB5ZSH354LSNBDDVANCNFSM4ODMM4PQ .

[diogomart]

Glad to know it works for you.

You can try without './' and see if it works or not. If not, then for x in $(ls); do echo './'$x; done > list.txt should do the trick.

[debanjansen48]

sir, IT WORKS.........

without "./" it works.....

This program is extremely 1st.......I am so happy......certainly it will make my life easy........wooaooo....... just docked 50 ligs within 2 to 3min with -nrun 10 options No other tools can bit it i sware ....my legs are moderately big with more than 5 rotatable bonds.... Other commercial and well known open source docking tools take minimum 20min or more....

I am sorry, but I think I should tell you.

it generates 50 .dlg file "docking1.dlg" file.... it's a tedious job for large library screening to open each and every .dlg file and note down the dock score, clustering info etc..

is there any trick to solve that.. if u dont mistake me.

Thanks again

On Wed, Oct 28, 2020 at 11:51 PM Diogo notifications@github.com wrote:

Glad to know it works for you.

You can try without './' and see if it works or not. If not, then for x in $(ls); do echo './'$x; done > list.txt should do the trick.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ccsb-scripps/AutoDock-GPU/issues/89#issuecomment-718121755, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4TIQCQWJKUHCUC6ISTSNBOKFANCNFSM4ODMM4PQ .

[diogomart]

Happy to hear you are happy with the speed! Just keep in mind that comparing the speed is meaningful only if the results are of comparable quality.

For analyzing many files I recommend the Python language.