ADL: hydrogens in ligand file

Rupal Chauhan chauhanrupal757 at gmail.com
Thu May 24 02:52:50 PDT 2012


Hello,

I'm using AutoDock for the first time, and I am just wondering if a
binding energy of -2.49 is good or bad? this was the best result (1_1)
generated, with the lowest binding energy.

Any help would be greatly appreciated.

-Ruapl Chauhan

On 5/23/12, Ragothaman Yennamalli <ragothaman at gmail.com> wrote:
> Thank you,
> This was most helpful.
>
> Thanks and Regards,
> Raghu
>
> On Wed, May 23, 2012 at 5:18 PM, Ruth Huey <rhuey at scripps.edu> wrote:
>
>> Hi,
>> By default, prepare_ligand4.py "cleans-up" by removing non-polar
>> hydrogens
>> and lone pairs AFTER adding charges but before writing pdbqt file.
>> If for some reason you want to preserve the non-polar hydrogens, change
>> the 'cleanup type' via the -U flag like this:
>>
>> prepare_ligand4.py -l test.mol2 -v -o test.pdbqt -A hydrogens  -U lps
>>
>>   Best wishes,
>>       Ruth
>>
>> PS: If you invoke prepare_ligand4.py with no arguments, you will see a
>> usage statement similar to this one:
>>
>> prepare_ligand4: ligand filename must be specified.
>> Usage: prepare_ligand4.py -l filename
>>
>>    Description of command...
>>         -l     ligand_filename (.pdb or .mol2 or .pdbq format)
>>    Optional parameters:
>>        [-v]    verbose output
>>        [-o pdbqt_filename] (default output filename is
>> ligand_filename_stem + .pdbqt)
>>        [-d]    dictionary to write types list and number of active
>> torsions
>>        [-A]    type(s) of repairs to make:
>>                 bonds_hydrogens, bonds, hydrogens (default is to do no
>> repairs)
>>        [-C]    do not add charges (default is to add gasteiger charges)
>>        [-p]    preserve input charges on atom type, eg -p Zn
>>               (default is not to preserve charges on any specific atom
>> type)
>>        [-U]    cleanup type:
>>                 nphs_lps, nphs, lps, '' (default is 'nphs_lps')
>>        [-B]    type(s) of bonds to allow to rotate
>>               (default sets 'backbone' rotatable and 'amide' +
>> 'guanidinium' non-rotatable)
>>        [-R]    index for root
>>        [-F]    check for and use largest non-bonded fragment (default is
>> not to do this)
>>        [-M]    interactive (default is automatic output)
>>        [-I]    string of bonds to inactivate composed of
>>                   of zero-based atom indices eg 5_13_2_10
>>                   will inactivate atoms[5]-atoms[13] bond
>>                               and atoms[2]-atoms[10] bond
>>                      (default is not to inactivate any specific bonds)
>>        [-Z]    inactivate all active torsions
>>                      (default is leave all rotatable active except amide
>> and guanidinium)
>>        [-g]    attach all nonbonded fragments
>>        [-s]    attach all nonbonded singletons:
>>                   NB: sets attach all nonbonded fragments too
>>                      (default is not to do this)
>>
>> ________________________________________
>> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On
>> Behalf Of Ragothaman Yennamalli [ragothaman at gmail.com]
>> Sent: Wednesday, May 23, 2012 2:54 PM
>> To: autodock at scripps.edu
>> Subject: ADL: hydrogens in ligand file
>>
>> HI,
>> The ligand file, I am using to generate a .pdbqt file has hydrogens added
>> to it. However, when I write the pdbqt file, the hydrogens are missing. I
>> tried in ADT and using the python script with -A option.
>> pythonsh
>>
>> /Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py
>> -l test.mol2 -v -o test.pdbqt -A 'hydrogens'
>> My question is how can I make sure the hydrogens do not get deleted in
>> the
>> .pdbqt file?
>>
>> Thanks and Regards,
>> Raghu
>> ________________________________________________
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>>
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