ADL: autodock Digest, Vol 46, Issue 3

jose correa corrjose at gmail.com
Thu Jan 10 06:26:21 PST 2008


Dear all
*Could you help me with the next points:*
**
*1)* How can i select *simulated annealing(SA)* algorithm in 'docking
parameter file step' using command line?

>pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt

this command help to use default lamarckian genetic algorithm(LGA) for
docking


>pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt -L -o LS_L.dpf

this command help to use local search(LS) algorithm for docking


> pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt -o GA.dpf -p
do_global_only=50 -p ga_run=0

this command line output(.dpf file) help me to select 'Genetic Algorithm' in
the autodock step.


How can i select simulated Annealing algorithm separately? I am not able to
find any supporting document also. Please help me in doing this.


*(2)* In the a Docking parameter file preparation step, have '-k' option for
specify the 'list of parameters to write'.

How '-k' option is used in command line? Whats its important? The usage or
description about this option is not provided.


*(3) *In the grid parameter file preparation step have '-d' option for
specify the 'directory of ligands to use to set types'.

What does '-d' option mean in detail?. Does it mean for specify the multiple
ligand directory?.


I tried following commands

>pythonsh prepare_gpf4.py -l ind.pdbqt -r hsg1.pdbqt

i got correct output for this command.


> pythonsh prepare_gpf4.py -l ind.pdbqt -r hsg1.pdbqt -o hsg1_d.gpf -d
/root/Desktop/AUTODOCK4/Testing_cmd/Grid-3 /pdbqt

/root/Desktop/AUTODOCK4/Testing_cmd/Grid-3 /pdbqt -> this directory contains
3 ligand files with .pdbqt format.

output (hsg1_d.gpf) file haven't no information about 'ligand_types' and
'map files'

*********************** hsg1_d.gpf**********************

npts 42 40 40 # num.grid points in xyz

gridfld hsg1.maps.fld # grid_data_file

spacing 0.375 # spacing(A)

receptor_types A C N NA OA SA # receptor atom types

ligand_types # ligand atom types

receptor hsg1.pdbqt # macromolecule

gridcenter auto # xyz-coordinates or auto

smooth 0.5 # store minimum energy w/in rad(A)

elecmap hsg1.e.map # electrostatic potential map

dsolvmap hsg1.d.map # desolvation potential map

dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant

****************end of hsg1_d.gpf**********************


How can i use '-d' option?. Please give me one command line example with
this option. No where in the document give its usage.

If '-d' option is not for specify the multiple ligand directory, then how
can i dock multiple ligand with one receptor? Is it need to run each script
for each ligand?. Or in autodock4 have any single script/command for run
multiple ligand ?

I am waiting for your response.



2008/1/7, autodock-request at scripps.edu <autodock-request at scripps.edu>:
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> Today's Topics:
>
>   1.  recurrent question: charge assignment (Jordi)
>   2.  Get the ligand information from dlg using AutoDock4 (Hao Tang)
>   3. Re:  Python Error-Jaya (Jayakanthan(Jacks))
>   4. Re:  Get the ligand information from dlg using AutoDock4
>      (Tee Pioj)
>   5. Re:  Get the ligand information from dlg using AutoDock4 (Yang Ye)
>   6.  Nitrogen atom types - NA or N? (Tomek Wlodarski)
>   7.  followup--> need help installing mgl frm source (Vinay Kumar)
>   8.  Doubt in 'docking parameter file preparation step'.
>      (Remya Francis M.)
>   9. Re:  recurrent question: charge assignment (Sargis Dallakyan)
> 10. Re:  Nitrogen atom types - NA or N? (Sargis Dallakyan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 4 Jan 2008 21:41:20 +0100
> From: "Jordi" <jbvqob at iiqab.csic.es>
> Subject: ADL: recurrent question: charge assignment
> To: <autodock at scripps.edu>
> Message-ID: <02ee01c84f12$29d6ae80$34df6fa1 at JORDIB>
> Content-Type: text/plain;       charset="iso-8859-1"
>
> Hi,
>
> Sorry if this is a recurrent question (I know it is...) but I think that
> many of us are a little confused about what charges should be used with
> Autodock 4. A few weeks ago, I read a post from G.M. Morris saying that
> Autodock 4 has been parameterized with Gasteiger charges either for the
> ligands and for the receptors and that using a different set of charges (ie.
> AMBER charges,....) is possible but it would require to calculate new
> parameters in order to achieve a good correlation between calculated and
> experimental DeltaG of binding. If this is correct (is it?) then it is
> obvious that Gasteiger's is the right choice if you don't want to do that
> extra work.
> However, when using Autodock Tools to assign Gasteiger charges to the
> receptor, it also changes the protonation and tautomer states to its
> defaults (ie. neutral HIS, negative ASP and GLU, positive LYS and ARG),
> screewing up any previous work done (out from ADT) to set those. Therefore,
> is there any way to avoid this? I know that ADT has a module that can be
> used to set the HIS protonation state but still is a pain if one has already
> done this with some other program and only wants to assign Gasteiger partial
> charges without changing anything else. I have tried to assign Gasteiger
> charges with different programs other than ADT but it seems that the results
> are not the same therefore are we forced to use ADT somehow?
>
> Thanks for any comments or clarifications.
>
> Jordi
>
> ------------------------------
>
> Message: 2
> Date: Fri, 04 Jan 2008 15:59:52 -0500
> From: Hao Tang <haotang1982 at gmail.com>
> Subject: ADL: Get the ligand information from dlg using AutoDock4
> To: autodock at scripps.edu
> Message-ID: <477E9E48.6060703 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
> I am a new user for AutoDock4. I have successfully generate the dlg file
> by using the ADT. And I can also visualize the docked molecules using
> ADT. But I want to extract the docked ligands in pdb format or (mol2,
> etc.) from the dlg file . Do anyone know how to do it?   I tried to use
> "get-docked  result.dlg " command, but it doesn't work. The system does
> not recognize get-docked command.
>
> Thank you very much in advance.
>
> Hao
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 5 Jan 2008 06:02:46 +0000 (GMT)
> From: "Jayakanthan\(Jacks\)" <info_jai at yahoo.com>
> Subject: Re: ADL: Python Error-Jaya
> To: autodock at scripps.edu
> Message-ID: <765401.15313.qm at web94506.mail.in2.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Thanks Mr. Sargis....
>
>
>
> Sargis Dallakyan <sargis at scripps.edu> wrote:
> > Anybody can help me pls. Recently I downloaded AUTODOCK4 along with ADT
> for windows OS. The problem is, whenever I am working with autodock4 tool,
> there is a widget displayed like ?Python.exe has encountered a problem and
> needs to close. We are sorry for the inconvenience? and closing this
> autodock4 tool with an option like ?sending error? and ?don?t send error?.
> Please anybody can suggest there is any option to overcome this problem.
>
> These messages are sent to Microsoft and I'm not sure if Microsoft and
> Python
> developers can fix the problem. You can disable the "Send an error report
> to
> Microsoft" message as described here:
> http://www.worldstart.com/tips/tips.php/598
>
> To help us solve your problem we need to have all the input files and
> steps to
> reproduce the bug.
> http://mgltools.scripps.edu/documentation/how-to/report-a-bug
> http://autodock.scripps.edu/faqs-help/faq/how-do-i-report-a-bug
>
> Thanks,
> Sargis
> ________________________________________________
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>                    With Regards,
> M. Jayakanthan M.Sc.,
> Junior Research Fellow,
> Centre for Bioinformatics
> School of Life Sciences
> Pondicherry University
> Puducherry - 605 014
> Phone: 09843696114
> E-mail : jai.dbt at gmail.com
> Web Site: http://www.geocities.com/info_jai
>
>
>
>
>
>
>
>
>
>
>
>
> ---------------------------------
> Chat on a cool, new interface. No download required. Click here.
>
> ------------------------------
>
> Message: 4
> Date: Sat, 5 Jan 2008 22:04:32 +0800 (CST)
> From: Tee Pioj <tee_piorj at yahoo.com>
> Subject: Re: ADL: Get the ligand information from dlg using AutoDock4
> To: autodock at scripps.edu
> Message-ID: <4659.38661.qm at web59303.mail.re1.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi!
> Your problem need setting environment variable. If you use bash shell, try
> following:
> In your home dir, type vi .bashrc and then copy these lines
>
>
> PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:$AUTODOCK_UTI:$AUTODOCK_BIN:$AUTODOCK_HOME
> AUTODOCK_BIN=/your_binary_dir_autodock (e.g. /usr/local/bin)
> AUTODOCK_UTI=/your_autodock_share_dir (e.g. /usr/local/dist305/src/)
> AUTODOCK_HOME=/your_autodock_dir (e.g. /usr/local/dist305/)
>
> export PATH
> export AUTODOCK_HOME
> export AUTODOCK_BIN
> export AUTODOCK_UTI
>
> type wq! to save and exit
> type source .bashrc (twice)
>
> type echo $PATH to check that
> usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:$AUTODOCK_UTI:$AUTODOCK_BIN:$AUTODOCK_HOME
> appear in the line.
>
> try to use get-docked again, it should work
> Good luck
>
> ----- Original Message ----
> From: Hao Tang <haotang1982 at gmail.com>
> To: autodock at scripps.edu
> Sent: Saturday, January 5, 2008 3:59:52 AM
> Subject: ADL: Get the ligand information from dlg using AutoDock4
>
> Hello,
> I am a new user for AutoDock4. I have successfully generate the dlg file
> by using the ADT. And I can also visualize the docked molecules using
> ADT. But I want to extract the docked ligands in pdb format or (mol2,
> etc.) from the dlg file . Do anyone know how to do it?  I tried to use
> "get-docked  result.dlg " command, but it doesn't work. The system does
> not recognize get-docked command.
>
> Thank you very much in advance.
>
> Hao
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
> ____________________________________________________________________________________
> Be a better friend, newshound, and
> know-it-all with Yahoo! Mobile.  Try it now.
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>
> ------------------------------
>
> Message: 5
> Date: Sun, 06 Jan 2008 00:02:32 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: ADL: Get the ligand information from dlg using AutoDock4
> To: autodock at scripps.edu
> Message-ID: <477FAA18.4050904 at yahoo.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> get-docked is part of ad3. you need to get it in order to use it.
>
> Regards,
> Yang Ye
>
> Hao Tang wrote:
> > Hello,
> > I am a new user for AutoDock4. I have successfully generate the dlg file
> > by using the ADT. And I can also visualize the docked molecules using
> > ADT. But I want to extract the docked ligands in pdb format or (mol2,
> > etc.) from the dlg file . Do anyone know how to do it?   I tried to use
> > "get-docked  result.dlg " command, but it doesn't work. The system does
> > not recognize get-docked command.
> >
> > Thank you very much in advance.
> >
> > Hao
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sat, 5 Jan 2008 23:21:12 +0100
> From: "Tomek Wlodarski" <tomek.wlodarski at gmail.com>
> Subject: ADL: Nitrogen atom types - NA or N?
> To: autodock at scripps.edu
> Message-ID:
>        <1ddbb3110801051421j1140b913h565389d597d1c0b7 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> I am new in this field so sorry if my question is to basic.
> I am using AutoDock4 with ADT and almost in every case when I try to make
> pdbqt file for my ligand all nitrogens are in N autodock atom type - so
> they
> can not be acceptor in hydrogen bond - but i do not understand why....??
> My question is when I can have NA and when N nitrogen type - when nitrogen
> can't be a hydrogen bond acceptor?
> All oxygen are in OA form, and this is ok for me - why the same situation
> is
> not in nitrogen case?
> In Tutorial it is used Indinavir as ligand and then:
>
> "Nitrogens which can accept hydrogen-bonds are assigned AutoDock
> type 'NA' while those which cannot are assigned 'N'. In
> indinavir, the AutoDock type of atom N5 in the heterocycle
> is 'NA' while the other nitrogens are assigned 'N'."
> Why only heterocycle?
>
> http://en.wikipedia.org/wiki/Indinavir
> I would be very grateful for help
> Best,
>
> Tomasz
>
>
> ------------------------------
>
> Message: 7
> Date: Sun, 6 Jan 2008 21:52:31 +0530
> From: "Vinay Kumar" <ksvinaykumar at gmail.com>
> Subject: ADL: followup--> need help installing mgl frm source
> To: autodock at scripps.edu
> Message-ID:
>        <ef4e9c1a0801060822w449a0a61t8c9338f9af34f2e1 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello Sargis,
> Well,  I was not able to overcome the problem with PIL, and am pretty
> sure i did not mess up the install by installing for a different
> architecture for tcl-devel. but figured a way around by using the
> precompiled versions from the link sent by you.
>
> so at present my lab workstation runs MGLtools. but, i would have
> preferred it would have installed from the source...
>
> Thanks a lot for your input.
>
> Vinay
> ps- the trials are not yet over. i shall keep trying to do the install
> from source. until i get through.
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 7 Jan 2008 17:06:55 +0530
> From: "Remya Francis M." <remyafrancis at gmail.com>
> Subject: ADL: Doubt in 'docking parameter file preparation step'.
> To: autodock at scripps.edu
> Message-ID:
>        <e12b98430801070336m21e02843x878820a04b8d1e5f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello  Sir,
>
> I am Remya Frsnics M, Delhi. Working in a Bioinformatics company.
>
> Sir, Now i am working in Autodock4(Command line). I have some doubt on it.
>
> I am stuck in the 'docking parameter file preparation step'.
>
> (1) How can i select one algorithm using command line?
>
> " *pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt -o
> Local_Search_Algo.dpf -L* "
>
> -L helps me in specifying only LocalSearch algorithm
>
> if i do not define anything then by default LGA is working
>
> i want to run docking only with simulated anealing or with genetic
> algorithm
> or with local search or with LGA. In this case i know how to run only LGA
> and Local Search but how to go separately for other two i am not able to
> specify. I am not able to find any supporting document also. *Please help
> me
> in doing this.*
>
>
> (2) How can I use "-k" option in the 'docking parameter file preparation
> step'?
>
>
> With Thanks & Regards,
>
> Remya Francis M.
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 07 Jan 2008 13:17:18 -0800
> From: Sargis Dallakyan <sargis at scripps.edu>
> Subject: Re: ADL: recurrent question: charge assignment
> To: autodock at scripps.edu
> Message-ID: <478296DE.30608 at scripps.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> > However, when using Autodock Tools to assign Gasteiger charges to the
> receptor, it also changes the protonation and tautomer states to its
> defaults (ie. neutral HIS, negative ASP and GLU, positive LYS and ARG),
> screewing up any previous work done (out from ADT) to set those. Therefore,
> is there any way to avoid this?
>
> Hi Jordi,
>
> Are you using Edit -> Charges -> Compute Gasteiger to assign Gasteiger
> charges
> to the receptor? If so, it is not supposed to add or remove any atom from
> the
> molecule. If, on the other hand, you are using Grid -> Macromolecule ->
> Choose,
> it does remove non-polar hydrogens, by default, but it should not mess up
> the
> protonation state of the residues you mentioned (ie. neutral HIS, negative
> ASP
> and GLU, positive LYS and ARG).
>
> I don't quite understand why this did not work in you case, that's why I'd
> recommend to use our Bugzilla http://mgldev.scripps.edu/bugs/ to submit a
> feature request. Please include input files, if any, as an attachment.
>
> Thanks,
> Sargis
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 07 Jan 2008 14:02:37 -0800
> From: Sargis Dallakyan <sargis at scripps.edu>
> Subject: Re: ADL: Nitrogen atom types - NA or N?
> To: autodock at scripps.edu
> Message-ID: <4782A17D.6080605 at scripps.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> > I am new in this field so sorry if my question is to basic.
> > I am using AutoDock4 with ADT and almost in every case when I try to
> make
> > pdbqt file for my ligand all nitrogens are in N autodock atom type - so
> they
> > can not be acceptor in hydrogen bond - but i do not understand why....??
> > My question is when I can have NA and when N nitrogen type - when
> nitrogen
> > can't be a hydrogen bond acceptor?
>
> Hi Tomasz,
>
> The following condition in AutoDockTools/atomTypeTools.py makes nitrogens
> hydrogen bond acceptor('N' + 'A')
>
>                 if item.babel_type in ['N3','N2','N1']:
>                     item.autodock_element = item.element + 'A'
>                 elif item.babel_type in ['Nam', 'Npl', 'Ng+']:
>                     if len(item.bonds)==2:
>                         item.autodock_element = item.element + 'A'
>
>
> Translated to English this means, nitrogen is acceptor if:
> it is sp1, sp2 or sp3 nitrogen, or
> it is nitrogen amide, trigonal planar or Ng+ (sp3 plus H+?), and its
> bonded to 2
> atoms.
>
> > "Nitrogens which can accept hydrogen-bonds are assigned AutoDock
> > type 'NA' while those which cannot are assigned 'N'. In
> > indinavir, the AutoDock type of atom N5 in the heterocycle
> > is 'NA' while the other nitrogens are assigned 'N'."
> > Why only heterocycle?
> >
> > http://en.wikipedia.org/wiki/Indinavir
>
> I used the following commands after reading ind.pdb and using Ligand ->
> Input ->
> Choose...:
> >>> mv.selectFromString(atoms='N*')
> >>> mv.selection.autodock_element
> ['N', 'N', 'N', 'N', 'NA']
> >>> mv.selection.babel_type
> ['N3+', 'Nam', 'Npl', 'Nam', 'Npl']
> >>> mv.selection.name
> ['N1', 'N2', 'N3', 'N4', 'N5']
>
> N5 in Indinavir is acceptor because its in the ring and bonded to 2 atoms.
>
> Hope this helps,
> Sargis
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 46, Issue 3
> ***************************************
>


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