ADL: Setting the backbone rigid with scripts

Stefano Forli forli at scripps.edu
Mon Oct 22 10:46:05 PDT 2012


Dinler,

On 10/22/2012 03:51 AM, Dinler Antunes wrote:
> Dear Stefano,
>
> Thank you very much for this very useful tip. Let me ask you one more
> thing. Why by default this script makes amide and guanidinium bonds to
> be non-rotatable?
Amides are a conjugated system with reduced torsion flexibility. To reduce complexity, the 
code assumes the ligand is in a low energy state (i.e. minimized), hence amides are in the 
trans conformation that's energetically more favorable. Moreover, AutoDock doesn't have a 
specific torsion term for them, so setting them rotatable could sample torsions angles 
that are not very representative.

Similarly, the guanidinium is a highly conjugated system, so it doesn't make much sense to 
make it flexible.
>
> When I use the ADT interface to prepare the ligand, I first click on "Make
> all rotatable bonds rotatable" and after on "Make peptide backbone bonds
> rotatable", to make sure I have all backbone rigid and all side chains
> flexible. In a given peptide that I'm using for tests, this generates a
> ligand.pdbqt with 20 active torsions.

>
> I tried the comand line (with -B "None") and it generates a ligand.pdbqt
> with 18 active torsions. This difference is because this script by default
> set as non-ratatable some side chain bonds. I wonder if I will have similar
> results in both cases.
Not knowing which side chains you're referring to it is hard to guess what happened.
You should check which rotatable bonds are missing and see which option from the command 
line can provide the same behavior as ADT.
>
> Best Regards.
>
> --
> Dinler Amaral Antunes
> PhD Student
> NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética
> Department of Genetics
> Federal University of Rio Grande do Sul - Brazil
>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sat, 20 Oct 2012 17:01:15 -0300
>> From: Dinler Antunes<dinler at gmail.com>
>> Subject: ADL: Setting the backbone rigid with scripts
>> To: autodock at scripps.edu
>> Message-ID:
>>          <CAEjxMVg_tA80WzvNin2rp=
>> m28z+0Sfe5YhmHswN5q-p4wMVS7Q at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear fellow subscribers,
>>
>> We have adopted a special docking procedure of a peptide ligand into a
>> receptor, in which we use the ligand backbone rigid, and the ligand
>> side-chains flexible (about 25 rotatable bonds). We are having good results
>> and this set up is really easy to select using the ADT interface, which has
>> a button with the option "make peptide backbone bonds non-rotable". Now I'm
>> trying to make a script to automate this steps, since I want to perform
>> this with several different peptides. I'm trying to use the python script
>> provided with MGLTools, "prepare_ligand4.py". However, I failed to find a
>> way to make the same selection (backbone rigid and side chains flexible)
>> using this script. I tried to think in a combination of -Z and -B, but I
>> can't specify each bond that I want to make flexible, since this will vary
>> depending on each peptide (I allways want to make side chains flexible, but
>> the side chains will have different bonds depending on the peptide
>> sequence).
>>
>> Any suggestions?
>>
>>
>> prepare_ligand4.py -l filename
>>
>>      Description of command...
>>           -l     ligand_filename
>>
>>      Optional parameters:
>>
>>          [-v]    verbose output
>>          [-o pdbqt_filename] (output filename)
>>          [-d]    dictionary to write types list and number of active
>> torsions
>>          [-A]    type(s) of repairs to make:
>>                   bonds_hydrogens, bonds, hydrogens
>>
>>          [-C]    do not add charges
>>          [-p]    preserve input charges on atom type, eg -p Zn
>>          [-U]    cleanup type:
>>                   nphs_lps, nphs, lps, ''
>>          [-B]    type(s) of bonds to allow to rotate
>>
>>          [-R]    index for root
>>          [-F]    check for and use largest non-bonded fragment (False)
>>          [-M]    interactive (default is automatic)
>>          [-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 '')
>>
>>          [-Z]    inactivate all active torsions
>>                        (default is leave active)
>>
>>
>> Thanks!
>>
>> --
>> Dinler Amaral Antunes
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Sat, 20 Oct 2012 16:38:29 -0700
>> From: Stefano Forli<forli at scripps.edu>
>> Subject: Re: ADL: Setting the backbone rigid with scripts
>> To: "autodock at scripps.edu"<autodock at scripps.edu>
>> Message-ID:<508335F5.6080200 at scripps.edu>
>> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>>
>> Dinler,
>>
>> you want to use the prepare_ligand4.py script with the '-B' option.
>> The command line you want to use is this:
>>
>>    prepare_ligand.py -l ligand.pdb -B "None"
>>
>> This should write the file 'ligand.pdbqt' in which the entire backbone is
>> rigid.
>> To be sure the ligand is formatted correctly, try to process the same
>> ligand with and
>> without the option and check the total active torsions in the first line
>> of the PDBQT.
>>
>> Happy dockings,
>>
>> Stefano
>>
>> On 10/20/2012 01:01 PM, Dinler Antunes wrote:
>>> Dear fellow subscribers,
>>>
>>> We have adopted a special docking procedure of a peptide ligand into a
>>> receptor, in which we use the ligand backbone rigid, and the ligand
>>> side-chains flexible (about 25 rotatable bonds). We are having good
>> results
>>> and this set up is really easy to select using the ADT interface, which
>> has
>>> a button with the option "make peptide backbone bonds non-rotable". Now
>> I'm
>>> trying to make a script to automate this steps, since I want to perform
>>> this with several different peptides. I'm trying to use the python script
>>> provided with MGLTools, "prepare_ligand4.py". However, I failed to find a
>>> way to make the same selection (backbone rigid and side chains flexible)
>>> using this script. I tried to think in a combination of -Z and -B, but I
>>> can't specify each bond that I want to make flexible, since this will
>> vary
>>> depending on each peptide (I allways want to make side chains flexible,
>> but
>>> the side chains will have different bonds depending on the peptide
>>> sequence).
>>>
>>> Any suggestions?
>>>
>>>
>>> prepare_ligand4.py -l filename
>>>
>>>       Description of command...
>>>            -l     ligand_filename
>>>
>>>       Optional parameters:
>>>
>>>           [-v]    verbose output
>>>           [-o pdbqt_filename] (output filename)
>>>           [-d]    dictionary to write types list and number of active
>> torsions
>>>           [-A]    type(s) of repairs to make:
>>>                    bonds_hydrogens, bonds, hydrogens
>>>
>>>           [-C]    do not add charges
>>>           [-p]    preserve input charges on atom type, eg -p Zn
>>>           [-U]    cleanup type:
>>>                    nphs_lps, nphs, lps, ''
>>>           [-B]    type(s) of bonds to allow to rotate
>>>
>>>           [-R]    index for root
>>>           [-F]    check for and use largest non-bonded fragment (False)
>>>           [-M]    interactive (default is automatic)
>>>           [-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 '')
>>>
>>>           [-Z]    inactivate all active torsions
>>>                         (default is leave active)
>>>
>>>
>>> Thanks!
>>>
>>> --
>>> Dinler Amaral Antunes
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>> --
>>    Stefano Forli, PhD
>>
>>    Staff Scientist
>>    Molecular Graphics Laboratory
>>    Dept. Molecular Biology,  MB-112F
>>    The Scripps Research Institute
>>    10550  North Torrey Pines Road
>>    La Jolla,  CA 92037-1000,  USA.
>>
>>       tel: (858) 784-2055
>>       fax: (858) 784-2860
>>       email: forli at scripps.edu
>>       http://www.scripps.edu/~forli/
>>
>>
>> ------------------------------
>>
>> ________________________________________________
>> --- ADL: AutoDock List  ---
>> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>>
>> End of autodock Digest, Vol 98, Issue 12
>> ****************************************
>>
>
>
>

-- 
  Stefano Forli, PhD

  Staff Scientist
  Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112F
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at scripps.edu
     http://www.scripps.edu/~forli/


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