ADL: error on parsing input file for docking

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ADL: error on parsing input file for docking

Ross KK Leung
Dear all:

 

I’m using Autodock Vina to perform large scale virtual screening. While some of the protein receptor files can be docked, some fail. Would you please suggest why running the attached files will result in error “Parse error on line 4444 in file "receptor.pdbqt": ATOM syntax incorrect: "f" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.”?

 

Thank you very much in advance!

 

Cheers, Ross


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--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

conf.txt (169 bytes) Download Attachment
receptor.pdbqt (385K) Download Attachment
ligand.pdbqt (7K) Download Attachment
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Re: ADL: error on parsing input file for docking

Ruth Huey
Replace 'f' at the end of line 4444 in receptor.pdbqt with the correct autodock_element for iron which is  "FE"

Change this line:
HETATM 4444 FE   HEM A1501      54.975  78.858  10.675  1.00 63.67     0.000 f

to

HETATM 4444 FE   HEM A1501      54.975  78.858  10.675  1.00 63.67     0.000 FE
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Ross KK Leung [[hidden email]]
Sent: Friday, May 09, 2014 3:06 AM
To: [hidden email]
Subject: ADL: error on parsing input file for docking

Dear all:



I’m using Autodock Vina to perform large scale virtual screening. While some of the protein receptor files can be docked, some fail. Would you please suggest why running the attached files will result in error “Parse error on line 4444 in file "receptor.pdbqt": ATOM syntax incorrect: "f" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.”?



Thank you very much in advance!



Cheers, Ross


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: error on parsing input file for docking

Ross KK Leung
Thank you Dr Ruth Huey. From your hint, I notice that many receptors
prepared by the following commands

/home/user1/mgltools_x86_64Linux2_1.5.6/bin/pythonsh prepare_receptor.py -r
$myline -A 'bonds_hydrogens'                    
base=`basename "$myline" .pdb`

/home/ user1/mgltools_x86_64Linux2_1.5.6/bin/pythonsh pdbqs_to_pdbqt.py -s
$base -C  

Produce invalid structures. I'm harnassing autodock vina for large scale
virtual screening. Do you happen to know if there is any prepared .pdbqt of
human proteins for docking? It would be terrible to manually validate
20,000+ human protein structures.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Ruth Huey
Sent: Saturday, May 10, 2014 5:32 AM
To: [hidden email]
Subject: Re: ADL: error on parsing input file for docking

Replace 'f' at the end of line 4444 in receptor.pdbqt with the correct
autodock_element for iron which is  "FE"

Change this line:
HETATM 4444 FE   HEM A1501      54.975  78.858  10.675  1.00 63.67     0.000
f

to

HETATM 4444 FE   HEM A1501      54.975  78.858  10.675  1.00 63.67     0.000
FE
________________________________________
From: [hidden email] [[hidden email]] On Behalf
Of Ross KK Leung [[hidden email]]
Sent: Friday, May 09, 2014 3:06 AM
To: [hidden email]
Subject: ADL: error on parsing input file for docking

Dear all:



I'm using Autodock Vina to perform large scale virtual screening. While some
of the protein receptor files can be docked, some fail. Would you please
suggest why running the attached files will result in error "Parse error on
line 4444 in file "receptor.pdbqt": ATOM syntax incorrect: "f" is not a
valid AutoDock type. Note that AutoDock atom types are case-sensitive."?



Thank you very much in advance!



Cheers, Ross


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: error on parsing input file for docking

Ruth Huey
When preparing input for Autodock Vina (or for Autodock4) use prepare_receptor4.py and prepare_ligand4.py.  
fyi: prepare_ligand.py and prepare_receptor.py generate input suitable for Autodock3
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Ross KK Leung [[hidden email]]
Sent: Sunday, May 11, 2014 9:28 PM
To: [hidden email]
Subject: Re: ADL: error on parsing input file for docking

Thank you Dr Ruth Huey. From your hint, I notice that many receptors
prepared by the following commands

/home/user1/mgltools_x86_64Linux2_1.5.6/bin/pythonsh prepare_receptor.py -r
$myline -A 'bonds_hydrogens'
base=`basename "$myline" .pdb`

/home/ user1/mgltools_x86_64Linux2_1.5.6/bin/pythonsh pdbqs_to_pdbqt.py -s
$base -C

Produce invalid structures. I'm harnassing autodock vina for large scale
virtual screening. Do you happen to know if there is any prepared .pdbqt of
human proteins for docking? It would be terrible to manually validate
20,000+ human protein structures.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Ruth Huey
Sent: Saturday, May 10, 2014 5:32 AM
To: [hidden email]
Subject: Re: ADL: error on parsing input file for docking

Replace 'f' at the end of line 4444 in receptor.pdbqt with the correct
autodock_element for iron which is  "FE"

Change this line:
HETATM 4444 FE   HEM A1501      54.975  78.858  10.675  1.00 63.67     0.000
f

to

HETATM 4444 FE   HEM A1501      54.975  78.858  10.675  1.00 63.67     0.000
FE
________________________________________
From: [hidden email] [[hidden email]] On Behalf
Of Ross KK Leung [[hidden email]]
Sent: Friday, May 09, 2014 3:06 AM
To: [hidden email]
Subject: ADL: error on parsing input file for docking

Dear all:



I'm using Autodock Vina to perform large scale virtual screening. While some
of the protein receptor files can be docked, some fail. Would you please
suggest why running the attached files will result in error "Parse error on
line 4444 in file "receptor.pdbqt": ATOM syntax incorrect: "f" is not a
valid AutoDock type. Note that AutoDock atom types are case-sensitive."?



Thank you very much in advance!



Cheers, Ross


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---