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 Post subject: virtual docking
PostPosted: Wed Jul 08, 2009 8:17 pm 
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Posts: 20
Hi

I was trying to do the virutal screening using vina, I did split the file in mol2 format and used prepare_ligand.py from adttools
to make pdbqt files.

while running the virutal docking,

>> conf.txt file

receptor = vk.pdb

center_x = 46.82
center_y = -45.78
center_z = 0.29

size_x = 122
size_y = 88
size_z = 80

energy_range = 4
exhaustiveness = 8

>> virtual screening

for f in NSC*.pdbqt; do
b=`basename $f .pdbqt`
echo Processing ligand $b
mkdir -p $b
./vina --config conf.txt --ligand $f --ligand_out ${b}/out_ --log ${b}/log.t
xt
done


>>
got following error messages

Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file

Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)

Configuration file (optional):
--config arg the above options can be put here

Information (optional):
--help print this message
--version print program version

Processing ligand NSC10003
Command line parse error: unknown option ligand_out

Correct usage:

Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)

over and over repeatly untill reads all the ligand and no results were seen except creating the subdirectories?

Not sure what is wrong? I did successfully used vina for virtual screening for small list of compounds.


Any help ?


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 Post subject: Re: virtual docking
PostPosted: Wed Jul 08, 2009 10:47 pm 
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Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
Quote:
Not sure what is wrong?


Please look for the line that says "error" and read what is says. This would have been the first line, had you copy-pasted correctly:

Command line parse error: unknown option ligand_out

I hope this is clear enough: "ligand_out" is not a valid option (since 1.0)

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 Post subject: Re: virtual docking
PostPosted: Wed Jul 08, 2009 10:59 pm 
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Joined: Wed Jun 24, 2009 2:28 am
Posts: 20
Thanks,

Here is the way I did run the virtual screen, named vir.txt as I attached before,


$ ./vir.txt | tee x.log
Processing ligand NSC10000
Command line parse error: unknown option ligand_out

Correct usage:

Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)

Search space (required):
--center_x arg X coordinate of the center
--center_y arg Y coordinate of the center
--center_z arg Z coordinate of the center
--size_x arg size in the X dimension (Angstroms)
--size_y arg size in the Y dimension (Angstroms)
--size_z arg size in the Z dimension (Angstroms)

Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file

Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)

Configuration file (optional):
--config arg the above options can be put here

Information (optional):
--help print this message
--version print program version

Processing ligand NSC10001
Command line parse error: unknown option ligand_out

Correct usage:

Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)

Search space (required):
--center_x arg X coordinate of the center
--center_y arg Y coordinate of the center
--center_z arg Z coordinate of the center
--size_x arg size in the X dimension (Angstroms)
--size_y arg size in the Y dimension (Angstroms)
--size_z arg size in the Z dimension (Angstroms)

Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file

Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)

Configuration file (optional):
--config arg the above options can be put here

Information (optional):
--help print this message
--version print program version

Processing ligand NSC10002
Command line parse error: unknown option ligand_out

Correct usage:

Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)

Search space (required):
--center_x arg X coordinate of the center
--center_y arg Y coordinate of the center
--center_z arg Z coordinate of the center
--size_x arg size in the X dimension (Angstroms)
--size_y arg size in the Y dimension (Angstroms)
--size_z arg size in the Z dimension (Angstroms)

Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file

Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)

Configuration file (optional):
--config arg the above options can be put here

Information (optional):
--help print this message
--version print program version

Processing ligand NSC10003
Command line parse error: unknown option ligand_out

>>>> etc.,



>>> Also did log file x.log that gave me the following text field

Processing ligand NSC10000
Processing ligand NSC10001
Processing ligand NSC10002
Processing ligand NSC10003
Processing ligand NSC10004
Processing ligand NSC10005
Processing ligand NSC10006
Processing ligand NSC10007
Processing ligand NSC10008
Processing ligand NSC10009
Processing ligand NSC1000
Processing ligand NSC10010
Processing ligand NSC10011
Processing ligand NSC10012
Processing ligand NSC10013
Processing ligand NSC10014
Processing ligand NSC10015

etc.,

After completion of all data it did not give any result just empty directory , guessing vina some how not running?

Also in the created sub directory, NSC10000, two files stderr, stdout
stderr : /var/spool/PBS/mom_priv/jobs/636417.master01.SC: line 3: vina: command not found
stdout : empty

Thanks
venkat


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 Post subject: Re: virtual docking
PostPosted: Thu Jul 09, 2009 6:05 pm 
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Joined: Wed Jun 24, 2009 2:28 am
Posts: 20
Dear Olgott

Thanks for the reply, I am using cluster and got the same error after downloaded the new vina.

my virtual docking file is
$./vir.txt

for f in *.pdbqt; do
b=`basename $f .pdbqt`
echo Processing ligand $b
mkdir -p $b
./vina --config conrigid.inp --ligand $f --ligand_out ${b}/out_ --log ${b}/log.txt
done

my conrigid.inp file is
more conrigid.inp
receptor = vk.pdbqt

center_x = 42.082
center_y = -49.24
center_z = 5.241

size_x = 10
size_y = 16
size_z = 10

energy_range = 4
exhaustiveness = 8


Same error ?

Processing ligand NSC10009
Command line parse error: unknown option ligand_out

also vina vesion
$ ./vina --version
AutoDock Vina 1.0.1 (Jun 24, 2009)

any help ?


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