ADL: Installing Autogrid/Autodock on Windows (via Cygwin)

Jérôme Baffreau jerome.baffreau at umontreal.ca
Mon Feb 9 09:39:25 PST 2009


Hello,

here you'll everything you need: 
http://autodock.scripps.edu/faqs-help/faq/installing-autodock-on-windows

You can do everything on Windows but running autogrid/autodock. To run 
autogrid/autodock on Windows, you first need to install Cygwin (pretty 
straightforward) then download autodock for Windows 
(http://autodock.scripps.edu/downloads), copy these 2 files into 
/usr/local/bin/ and you're done!

Regards,
Jerome


--------------------------------------------------
From: "bijit bhowmik" <bijitbhowmik at gmail.com>
Sent: Sunday, February 08, 2009 10:59 AM
To: <autodock at scripps.edu>
Subject: Re: ADL: autodock Digest, Vol 54, Issue 7

> Hello friends.
> I have been told that to run autodock in Win XP I need real or emulated
> Linus os. Can anybody tell me how can I get emulated linus background.
> Thanking all
> Bijit Kumar Bhowmik
>
> On Fri, Feb 6, 2009 at 12:28 PM, <autodock-request at scripps.edu> wrote:
>
>> Send autodock mailing list submissions to
>>        autodock at scripps.edu
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>        http://mgldev.scripps.edu/mailman/listinfo/autodock
>> or, via email, send a message with subject or body 'help' to
>>        autodock-request at scripps.edu
>>
>> You can reach the person managing the list at
>>        autodock-owner at scripps.edu
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of autodock digest..."
>>
>>
>> Today's Topics:
>>
>>   1.  running adt on Windows XP (bijit bhowmik)
>>   2. Re:  running adt on Windows XP (Jerome Baffreau)
>>   3. Re:  running adt on Windows XP (Samerene Siddique)
>>   4. Re:  autodock Digest, Vol 54, Issue 5 (thaniks)
>>   5. Re:  Process not running (annalisa bordogna)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 6 Feb 2009 10:14:17 +0530
>> From: bijit bhowmik <bijitbhowmik at gmail.com>
>> Subject: ADL: running adt on Windows XP
>> To: autodock at scripps.edu
>> Message-ID:
>>        <22e65be40902052044h4e653403l804e0dc305ff02b2 at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hello everybody,
>> I am relatively new in this field. Before performing docking can anybody
>> tell me whether ADT runs well in Windows XP because I heard before this 
>> is
>> for Linus os.Plz reply ASAP.
>> Regards,
>> Bijit Kr. Bhowmik
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 5 Feb 2009 21:17:08 -0800 (PST)
>> From: Jerome Baffreau <jerome.baffreau at umontreal.ca>
>> Subject: Re: ADL: running adt on Windows XP
>> To: autodock at scripps.edu
>> Message-ID: <1233897428829-2279246.post at n2.nabble.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>>
>> Hi,
>>
>> ADT runs fine on WinXP, but you won't be able to run autogrid or autodock
>> unless you install Cygwin on your computer.
>> This means you'll be able to prepare your calculations and process the
>> results, but you'll need a Linux environment (real or emulated) to run
>> Autodock calculations.
>>
>> Regards,
>> Jerome
>>
>>
>> bijit bhowmik wrote:
>> >
>> > Hello everybody,
>> > I am relatively new in this field. Before performing docking can 
>> > anybody
>> > tell me whether ADT runs well in Windows XP because I heard before this
>> is
>> > for Linus os.Plz reply ASAP.
>> > Regards,
>> > Bijit Kr. Bhowmik
>> > ________________________________________________
>> > --- ADL: AutoDock List  ---  
>> > http://autodock.scripps.edu/mailing_list ---
>> >
>> >
>>
>>
>> -----
>> Jerome
>>
>> ????????????????????????????????????????????
>> Jerome Baffreau, PhD
>> Universite de Montreal
>> Montreal, QC - CANADA
>>
>> --
>> View this message in context:
>> http://n2.nabble.com/ADL%3A-running-adt-on-Windows-XP-tp2279183p2279246.html
>> Sent from the AutoDock mailing list archive at Nabble.com.
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 6 Feb 2009 05:35:31 -0000 (GMT)
>> From: "Samerene Siddique" <sas1069 at londonmet.ac.uk>
>> Subject: Re: ADL: running adt on Windows XP
>> To: autodock at scripps.edu
>> Message-ID:
>> 
>> <88a67f25acc4c39831cddbea019240f2.squirrel at webmail2.londonmet.ac.uk
>> >
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> hi,
>>
>> n can u plzz tell me how do we use python scripts in window xp for
>> docking??
>>
>>
>>
>>
>>
>>
>>
>>
>> > Hi,
>> >
>> > ADT runs fine on WinXP, but you won't be able to run autogrid or 
>> > autodock
>> > unless you install Cygwin on your computer.
>> > This means you'll be able to prepare your calculations and process the
>> > results, but you'll need a Linux environment (real or emulated) to run
>> > Autodock calculations.
>> >
>> > Regards,
>> > Jerome
>> >
>> >
>> > bijit bhowmik wrote:
>> >>
>> >> Hello everybody,
>> >> I am relatively new in this field. Before performing docking can 
>> >> anybody
>> >> tell me whether ADT runs well in Windows XP because I heard before 
>> >> this
>> >> is
>> >> for Linus os.Plz reply ASAP.
>> >> Regards,
>> >> Bijit Kr. Bhowmik
>> >> ________________________________________________
>> >> --- ADL: AutoDock List  ---  
>> >> http://autodock.scripps.edu/mailing_list---
>> >>
>> >>
>> >
>> >
>> > -----
>> > Jerome
>> >
>> >
>> ????????????????????????????????????????????????????????????????????????????????????????
>> > Jerome Baffreau, PhD
>> > Universite de Montreal
>> > Montreal, QC - CANADA
>> >
>> > --
>> > View this message in context:
>> >
>> http://n2.nabble.com/ADL%3A-running-adt-on-Windows-XP-tp2279183p2279246.html
>> > Sent from the AutoDock mailing list archive at Nabble.com.
>> >
>> >
>> > ________________________________________________
>> > --- ADL: AutoDock List  ---  
>> > http://autodock.scripps.edu/mailing_list ---
>>
>>
>>
>>
>> Companies Act 2006 : http://www.londonmet.ac.uk/companyinfo
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 6 Feb 2009 11:29:54 +0530
>> From: thaniks <kthanikasalam at gmail.com>
>> Subject: Re: ADL: autodock Digest, Vol 54, Issue 5
>> To: autodock at scripps.edu
>> Message-ID:
>>        <a2e182280902052159y28f24760r3581ad6cc511e671 at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> > Dear Mr. Jerome,
>>
>>                 Thanks for your nice reply, Now i understand the problem,
>> Please let me know how to correct the charge of phosphate group to +2 in
>> pdbqt file. I really need your help to solve this problem.
>>
>> Thaniks
>>
>>
>>
>> >
>> > Message: 3
>> > Date: Wed, 4 Feb 2009 22:13:49 -0800 (PST)
>> > From: Jerome Baffreau <jerome.baffreau at umontreal.ca>
>> > Subject: Re: ADL: autodock Digest, Vol 54, Issue 4
>> > To: autodock at scripps.edu
>> > Message-ID: <1233814429327-2273457.post at n2.nabble.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> >
>> > Hi Thaniks,
>> >
>> > I had the same problem 2 weeks ago, here is the 2 answers I got:
>> >
>> > ############################
>> >
>> > Even orthophosphate has a pKa2 of ~6.8 (at 0.1 ionic strength). Most
>> > compounds
>> > with phosphoryl groups that I've seen pKa's reported for have pKa2's of
>> > ~5-6,
>> > so they would be predominately dianionic at neutral pH.  Also, don't
>> forget
>> > the context of the bound ligand -  a phosphate binding site would tend 
>> > to
>> > have a lot of positively charged groups (his, arg, lys, metal ions). 
>> > That
>> > sort of environment would lower the pKa of the bound phosphoryl moiety
>> > significantly. IMHO, these considerations imply dianionic, completely
>> > deprotonated phosphoryl groups at physiological pH.
>> >
>> >
>> > Regards,
>> >
>> > Mark
>> >
>> > On Monday 19 January 2009 10:04:24 am Rudy J. Richardson wrote:
>> > > To whom it may concern:
>> > >
>> > > At physiological pH, shouldn't the formal charge on a phosphate group
>> be
>> > > -1?
>> > >
>> > > Sincerely yours,
>> > >
>> > > Rudy
>> > >
>> > > ----------------------------------------------------
>> > > Rudy J. Richardson, ScD, DABT
>> > > Dow Professor of Toxicology
>> > > Associate Professor of Neurology
>> > > The University of Michigan
>> > > 1420 Washington Heights
>> > > Room M7525 SPH-II 2029
>> > > Ann Arbor, MI 48109-2029 USA
>> > >
>> > > Tel: (734) 936-0769 (office)
>> > > Tel: (734) 764-7156 (lab)
>> > > Tel: (734) 936-0782 (lab)
>> > > Fax: (734) 763-8095
>> > > Email: rjrich at umich.edu
>> >
>> > #################################
>> >
>> > Now I'm using phosphate groups with 2 charges and everything runs fine.
>> >
>> > Regards,
>> > Jerome
>> >
>> >
>> > thaniks wrote:
>> > >
>> > > Hi,
>> > >          I have one problem while using autodock. while i am trying 
>> > > to
>> > > dock
>> > > some ligands with phosphate group, autodock showed charge error.
>> without
>> > > phosphate group of the same ligand it did not show any charge error.
>> > > please
>> > > let me know how to correct this problem, any help in this is greatly
>> > > acknowledged.
>> > >
>> > > thaniks
>> > >
>> > >
>> > > On Thu, Feb 5, 2009 at 1:30 AM, <autodock-request at scripps.edu> wrote:
>> > >
>> > >> Send autodock mailing list submissions to
>> > >>        autodock at scripps.edu
>> > >>
>> > >> To subscribe or unsubscribe via the World Wide Web, visit
>> > >>        http://mgldev.scripps.edu/mailman/listinfo/autodock
>> > >> or, via email, send a message with subject or body 'help' to
>> > >>        autodock-request at scripps.edu
>> > >>
>> > >> You can reach the person managing the list at
>> > >>        autodock-owner at scripps.edu
>> > >>
>> > >> When replying, please edit your Subject line so it is more specific
>> > >> than "Re: Contents of autodock digest..."
>> > >>
>> > >>
>> > >> Today's Topics:
>> > >>
>> > >>   1.  how to start? (radhika ramachandran)
>> > >>   2.  Autodock and amber FF (Khaled Barakat)
>> > >>   3.  Autodock and amber FF (Khaled Barakat)
>> > >>
>> > >>
>> > >> ----------------------------------------------------------------------
>> > >>
>> > >> Message: 1
>> > >> Date: Wed, 4 Feb 2009 11:24:49 +0530
>> > >> From: radhika ramachandran <radhu03 at gmail.com>
>> > >> Subject: ADL: how to start?
>> > >> To: autodock at scripps.edu
>> > >> Message-ID:
>> > >>        <15b09d160902032154p56e025a2w38caaa7dcb90b7c9 at mail.gmail.com>
>> > >> Content-Type: text/plain; charset=ISO-8859-1
>> > >>
>> > >> I have installed Autodock4 in linux environment and i am not sure
>> about
>> > >> how
>> > >> to enter into the working environment and what command lines should 
>> > >> be
>> > >> used.
>> > >> --
>> > >> Radhika.R
>> > >>
>> > >>
>> > >> ------------------------------
>> > >>
>> > >> Message: 2
>> > >> Date: Tue, 3 Feb 2009 18:32:07 -0700
>> > >> From: "Khaled Barakat" <kbarakat at phys.ualberta.ca>
>> > >> Subject: ADL: Autodock and amber FF
>> > >> To: autodock at scripps.edu
>> > >> Message-ID: <200902040132.n141W7G15713 at webmail.phys.ualberta.ca>
>> > >> Content-Type: text/plain; charset=iso-8859-1
>> > >>
>> > >>
>> > >> Hello,
>> > >>
>> > >> Is there a possibility to run autodock with one of the amber force
>> > fields
>> > >> (for
>> > >> example the amber99sb force field)?
>> > >>
>> > >> khaled
>> > >>
>> > >>
>> > >> ------------------------------
>> > >>
>> > >> Message: 3
>> > >> Date: Tue, 3 Feb 2009 18:58:09 -0700
>> > >> From: "Khaled Barakat" <kbarakat at phys.ualberta.ca>
>> > >> Subject: ADL: Autodock and amber FF
>> > >> To: autodock at scripps.edu
>> > >> Message-ID: <200902040158.n141w9N16166 at webmail.phys.ualberta.ca>
>> > >> Content-Type: text/plain; charset=iso-8859-1
>> > >>
>> > >>
>> > >> Hello,
>> > >>
>> > >> Is there a possibility to run autodock with one of the amber force
>> > fields
>> > >> (for
>> > >> example the amber99sb force field)?
>> > >>
>> > >> khaled
>> > >>
>> > >>
>> > >> ------------------------------
>> > >>
>> > >> ________________________________________________
>> > >> --- ADL: AutoDock List  ---
>> > >> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>> > >>
>> > >> End of autodock Digest, Vol 54, Issue 4
>> > >> ***************************************
>> > >>
>> > >
>> > >
>> > >
>> > > --
>> > > with thanks and love
>> > >
>> > > K. Thanikasalam
>> > > Research Associate
>> > > Department of Chemistry
>> > > Indian Institute of Technology - Madras
>> > > Chennai
>> > >
>> > >
>> > > Ph. No. 09994559987 (mob)
>> > > ________________________________________________
>> > > --- ADL: AutoDock List  ---  
>> > > http://autodock.scripps.edu/mailing_list---
>> > >
>> > >
>> >
>> >
>> > -----
>> > Jerome
>> >
>> > ????????????????????????????????????????????
>> > Jerome Baffreau, PhD
>> > Universite de Montreal
>> > Montreal, QC - CANADA
>> >
>> > --
>> > View this message in context:
>> >
>> http://n2.nabble.com/Re%3A-ADL%3A-autodock-Digest%2C-Vol-54%2C-Issue-4-tp2273354p2273457.html
>> > Sent from the AutoDock mailing list archive at Nabble.com.
>> >
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Thu, 05 Feb 2009 17:34:15 +1030
>> > From: Nathan Stanley <nathan.stanley at adelaide.edu.au>
>> > Subject: ADL: Python Memory Error
>> > To: autodock at scripps.edu
>> > Message-ID: <498A8F6F.1010801 at adelaide.edu.au>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> > I'm getting an error when attempting to analyse dockings. I only get
>> > this error for certain macromolecules, whilst with others there is no
>> > problem. I'm running MGL Tools 1.5.2 on a Windows XP machine with 
>> > Python
>> > 2.5. I can view the clusterings, however when I select
>> > Analyse/Dockings/View Interactions, I get the following error and
>> > nothing happens. Any help would be greatly appreciated!
>> >
>> > Regards,
>> > Nathan
>> >
>> >
>> > ERROR *********************************************
>> > Traceback (most recent call last):
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\ViewerFramework\VF.py", line 716, in tryto
>> >    result = apply( command, args, kw )
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\AutoDockTools\autoanalyzeCommands.py", line 2087, 
>> > in
>> > doit
>> >    self.build()
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\AutoDockTools\autoanalyzeCommands.py", line 1912, 
>> > in
>> > build
>> >    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\MolKit\interactionDescriptor.py", line 46, in
>> __init__
>> >    self.build(detect_pi=detect_pi)
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\MolKit\interactionDescriptor.py", line 56, in build
>> >    self.buildCloseContactAtoms(percentCutoff)              #
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\MolKit\interactionDescriptor.py", line 65, in
>> > buildCloseContactAtoms
>> >    self.macro_atoms, percentCutoff=percentCutoff)
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\MolKit\distanceSelector.py", line 106, in select
>> >    bigC = Numeric.resize(c, (lenC, lenC, 3))
>> >  File "C:\Program Files\MGLTools
>> > 1.5.2\MGLToolsPckgs\numpy\core\fromnumeric.py", line 541, in resize
>> >    a = concatenate( (a,)*n_copies)
>> > MemoryError
>> >
>> >
>> > --
>> >
>> > Nathan Stanley - BSc (Hons)
>> > G04, Badger Building,
>> > Discipline of Chemistry,
>> > School of Chemistry & Physics,
>> > The University of Adelaide
>> > Adelaide
>> > South Australia, 5005
>> >
>> > Ph +61 8 8303 5360
>> > Fax +61 8 8303 4358
>> > Mob 0404 611 499
>> > nathan.stanley at adelaide.edu.au
>> > CRICOS Provider Number 00123M
>> > ----------------------------------------------------------- This email
>> > message is intended only for the addressee(s) and contains information
>> that
>> > may be confidential and/or copyright.  If you are not the intended
>> recipient
>> > please notify the sender by reply email and immediately delete this
>> email.
>> > Use, disclosure or reproduction of this email by anyone other than the
>> > intended recipient(s) is strictly prohibited. No representation is made
>> that
>> > this email or any attachments are free of viruses. Virus scanning is
>> > recommended and is the responsibility of the recipient.
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 5
>> > Date: Thu, 5 Feb 2009 09:19:00 +0100
>> > From: annalisa bordogna <annalisa.bordogna at gmail.com>
>> > Subject: ADL:  Process not running
>> > To: autodock at scripps.edu
>> > Message-ID:
>> >        <c61d325e0902050019t5aeba3d6uf26ba1331c02b34b at mail.gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > Hi everybody!
>> >
>> > I am running an autodock calculation on rockscluster, using pbs.
>> > For the run, I selected LGA with the creation of 300 poses.
>> > Now, when I do qstat -an1 to visualize the state of my job, it says 
>> > that
>> > it's running, but when I look into the .dlg file, it seems it has 
>> > stopped
>> > yesterday...
>> > I mean, the end of my file is:
>> >
>> > Generation: 22900   Oldest's energy: -10.369    Lowest energy: -10.369
>> > Num.evals.: 21649781   Timing: Real= 0.03s,  CPU= 0.03s,  System= 0.00s
>> > Generation: 23000   Oldest's energy: -10.369    Lowest energy: -10.369
>> > Num.evals.: 21746598   Timing: Real= 0.02s,  CPU= 0.02s,  System= 0.00s
>> > Generation: 23100   Oldest's energy: -10.369    Lowest energy: -10.369
>> > Num.evals.: 21847307   Timing: Real= 0.03s,  CPU= 0.03s,  System= 0.00s
>> >
>> > as if it were all ok and the process were still running, but the time 
>> > of
>> > creation of the latest pose is: Date:    Wed Feb  4 13:09:36 2009
>> > (Now, in my timezone, is Feb 5 9:15:00)
>> >
>> > Can somebody tell me what this means? I don't feel like to kill the 
>> > job,
>> > because it took 200 hours till now (it has generated 210 poses) and I'd
>> > like
>> > to make AutoDock perform the complete run without restarting it...
>> >
>> > Thank you very much!
>> > Annalisa
>> > ____________________________________
>> >
>> > Annalisa Bordogna - PhD. Student
>> > DISAT
>> > Universit? degli Studi di Milano - Bicocca
>> > Milano (Italy)
>> > ____________________________________
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 6
>> > Date: Thu, 05 Feb 2009 09:27:52 +0100
>> > From: Jean DESSOLIN <j.dessolin at iecb.u-bordeaux.fr>
>> > Subject: ADL: write_conformations_from_dlg.py
>> > To: autodock at scripps.edu
>> > Message-ID: <498AA308.6070701 at iecb.u-bordeaux.fr>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> > Hello Everybody,
>> >
>> > I found out what I believe to be a small bug in the script
>> > 'write_conformations_from_dlg.py' that belongs to MGL Tools.
>> >
>> > When I wish to extract the conformers obtained after a docking and 
>> > apply
>> > this script on my *.dlg, I obtain a number of files corressponding to
>> > the number of runs, but the termination of each file is shifted:
>> > -the last line of file 1 is at the beginning of file 2 and so on
>> > -at file 5, it's several lines from the end of file 4 that are present,
>> > and several lines from ligand 5 are missing....
>> >
>> > I still can 'cat' the files and separate these, but I believe the 
>> > script
>> > could easily be improved, unfortunately, I am not a python scripter.
>> >
>> > Since I'm talking about it, when using flexible residues, these are
>> > present at the end of the extracted ligand files, should'nt it be
>> > possible to replace these on the rigid receptor with a script that take
>> > into account the rigid part of the protein ? Something like:
>> > 'write_conformations_from_dlg.py -d your_result.dlg -r
>> > your_rigid_receptor.pdbqt
>> >
>> > and this could directly give an ensemble of ligand_1.pdbqt +
>> > reconstituted_receptor_1.pdbqt
>> >
>> > This might be quite helpful for those who wish to re-score the results.
>> >
>> > Many thanks in advance.
>> >
>> > Cheers.
>> >
>> > Jean
>> >
>> > --
>> > Dr. Jean DESSOLIN
>> >
>> > http://www.iecb.u-bordeaux.fr/
>> > j.dessolin at iecb.u-bordeaux.fr
>> > Institut Europ?en de Chimie et Biologie (IECB)
>> > CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets 
>> > (CBMN)
>> > 2, rue Robert Escarpit
>> > 33607 Pessac Cedex
>> > FRANCE
>> > T?l : 33 (0)5 40 00 30 29
>> > Fax : 33 (0)5 40 00 22 15
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 7
>> > Date: Thu, 05 Feb 2009 17:48:45 +0800
>> > From: qidiaoxiaoyao71 at sina.com
>> > Subject: ADL: Could single Mn2+ ion be used as ligand in Autodock?
>> > To: autodock at scripps.edu
>> > Message-ID:
>> >        <20090205094845.763BA1088033 at mail3-49.sinamail.sina.com.cn>
>> > Content-Type: text/plain;       charset=GBK
>> >
>> > Dear all:
>> > &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;I wand to perform some Docking job
>> with
>> > AutoDock. I wonder about could a manganese (Mn2+) ion be used as 
>> > ligand?
>> We
>> > tried once but the results seems weird for the Mn ion far away from the
>> > surface of&nbsp; Protein.&nbsp; Would you like give me some suggestion?
>> We
>> > wonder that&nbsp;is Autodock suitable for this kind of task?
>> > And&nbsp;&nbsp;is there any&nbsp;difference in&nbsp; method from 
>> > docking
>> > with small organic ligands.
>> > &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thank you for your
>> >
>> attention.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
>> >
>> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
>> > Your sincerely
>> >
>> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Yao
>> > Qi&nbsp;
>> >
>> > -------------------------------------------------------------------
>> > ???????????????????(http://space.sina.com.cn/ )
>> >
>> > ------------------------------
>> >
>> > ________________________________________________
>> > --- ADL: AutoDock List  ---
>> > http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>> >
>> > End of autodock Digest, Vol 54, Issue 5
>> > ***************************************
>> >
>>
>>
>>
>> --
>> with thanks and love
>>
>> K. Thanikasalam
>> Research Associate
>> Department of Chemistry
>> Indian Institute of Technology - Madras
>> Chennai
>>
>>
>> Ph. No. 09994559987 (mob)
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Fri, 6 Feb 2009 07:58:19 +0100
>> From: annalisa bordogna <annalisa.bordogna at gmail.com>
>> Subject: Re: ADL: Process not running
>> To: "M. Shahid" <mohammad.shahid at gmail.com>
>> Cc: autodock at scripps.edu
>> Message-ID:
>>        <c61d325e0902052258y671a6679r330becb496be67ba at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>>
>> it had taken some time, to me, to discover what the problem was (I 
>> haven't
>> a
>> system administrator, so I always have to study before knowing what's 
>> going
>> on with my cluster!): it seems that the nodes of my cluster have shut 
>> down
>> (maybe a problem with the electricity supply) and then restarted in a bad
>> way, so the process (in theory) is still running, but the nodes don't
>> recognize it anymore.
>> So, it is more or less as you said.
>>
>> Thank you very much for your answer,
>> best regards,
>> Annalisa
>> ____________________________________
>>
>> Annalisa Bordogna - PhD. Student
>> DISAT
>> Universit? degli Studi di Milano - Bicocca
>> Milano (Italy)
>> ____________________________________
>>
>>
>>
>> 2009/2/5 M. Shahid <mohammad.shahid at gmail.com>
>>
>> > Hi,
>> >
>> > To me its looking like a problem in the PBS system, that the job is 
>> > shown
>> > running but
>> > is actually not running. Please ask your system administrators or check
>> the
>> > log files (stdout/stderr)
>> > of your jobs. Long ago, I had a similar problem, but then it was due to
>> > hardware problem in the cluster machines...
>> >
>> > Best regards,
>> >
>> > --
>> > Shahid.
>> >
>> > On Thu, Feb 5, 2009 at 9:19 AM, annalisa bordogna <
>> > annalisa.bordogna at gmail.com> wrote:
>> >
>> >> Hi everybody!
>> >>
>> >> I am running an autodock calculation on rockscluster, using pbs.
>> >> For the run, I selected LGA with the creation of 300 poses.
>> >> Now, when I do qstat -an1 to visualize the state of my job, it says 
>> >> that
>> >> it's running, but when I look into the .dlg file, it seems it has
>> stopped
>> >> yesterday...
>> >> I mean, the end of my file is:
>> >>
>> >> Generation: 22900   Oldest's energy: -10.369    Lowest energy: -10.369
>> >> Num.evals.: 21649781   Timing: Real= 0.03s,  CPU= 0.03s,  System= 
>> >> 0.00s
>> >> Generation: 23000   Oldest's energy: -10.369    Lowest energy: -10.369
>> >> Num.evals.: 21746598   Timing: Real= 0.02s,  CPU= 0.02s,  System= 
>> >> 0.00s
>> >> Generation: 23100   Oldest's energy: -10.369    Lowest energy: -10.369
>> >> Num.evals.: 21847307   Timing: Real= 0.03s,  CPU= 0.03s,  System= 
>> >> 0.00s
>> >>
>> >> as if it were all ok and the process were still running, but the time 
>> >> of
>> >> creation of the latest pose is: Date:    Wed Feb  4 13:09:36 2009
>> >> (Now, in my timezone, is Feb 5 9:15:00)
>> >>
>> >> Can somebody tell me what this means? I don't feel like to kill the 
>> >> job,
>> >> because it took 200 hours till now (it has generated 210 poses) and 
>> >> I'd
>> >> like
>> >> to make AutoDock perform the complete run without restarting it...
>> >>
>> >> Thank you very much!
>> >> Annalisa
>> >> ____________________________________
>> >>
>> >> Annalisa Bordogna - PhD. Student
>> >> DISAT
>> >> Universit? degli Studi di Milano - Bicocca
>> >> Milano (Italy)
>> >> ____________________________________
>> >> ________________________________________________
>> >> --- ADL: AutoDock List  ---  
>> >> http://autodock.scripps.edu/mailing_list---
>> >>
>> >
>> >
>>
>>
>> ------------------------------
>>
>> ________________________________________________
>> --- ADL: AutoDock List  ---
>> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>>
>> End of autodock Digest, Vol 54, Issue 7
>> ***************************************
>>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---  



More information about the autodock mailing list