ADL: autodock Digest, Vol 39, Issue 6

jose correa corrjose at gmail.com
Wed Jun 6 06:04:50 PDT 2007


2007/6/6, autodock-request at scripps.edu <autodock-request at scripps.edu>:
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> Today's Topics:
>
>   1.  (no subject) (Elena Dolghih)
>   2.  PMV crashes upon opening (Elena Dolghih)
>   3. Re:  PMV crashes upon opening (hassan shallal)
>   4.  Auto Gridcenter in autodock 4 (snoze pa)
>   5.  AUTDOCK & BOINC (Jack Shultz)
>   6.  Excercise Problem (David Harrison)
>   7.  about autodock4 (hua wang)
>   8. Re:  Auto Gridcenter in autodock 4 (Yang Ye)
>   9.  Installation Help (David Harrison)
>  10.   pdb/dlg sorted by docked Energies (Joan Teyra)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Jun 2007 15:17:19 -0400
> From: "Elena Dolghih" <ldolghih at gmail.com>
> Subject: ADL: (no subject)
> To: autodock at scripps.edu
> Message-ID:
>        <4a2908460706051217o7ac98715k32be8bf165b50df0 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
>
> I have a problem with running PMV.
>
> After editing my .kshrc file following the installation instructions, I type
> pmv
> in the command line and can
> see PMV window open and then crash with the following message:
>
>
> linx32% pmv
> setting PYTHONHOME environment
> Run PMV from  /ufl/qtp/jlk/ld/MGLTools-1.4.5/MGLToolsPckgs/Pmv
> X Error of failed request:  GLXUnsupportedPrivateRequest
>  Major opcode of failed request:  152 (GLX)
>  Minor opcode of failed request:  17 (X_GLXVendorPrivateWithReply)
>  Serial number of failed request:  780
>  Current serial number in output stream:  780
>
>  With 1.4.4 release i get it to load and work half of the time but with
> 1.4.5
> release it doesn't load past 1%.
>
>  Does anybody have a suggestion about what is causing this and how to deal
> with
> it?
>
>  Appreciate any help,
>
>  Lena
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 5 Jun 2007 15:17:57 -0400
> From: "Elena Dolghih" <ldolghih at gmail.com>
> Subject: ADL: PMV crashes upon opening
> To: autodock at scripps.edu
> Message-ID:
>        <4a2908460706051217h7b176845wbd4530bd3c0c746a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
>
> I have a problem with running PMV.
>
> After editing my .kshrc file following the installation instructions, I type
> pmv
> in the command line and can
> see PMV window open and then crash with the following message:
>
>
> linx32% pmv
> setting PYTHONHOME environment
> Run PMV from  /ufl/qtp/jlk/ld/MGLTools-1.4.5/MGLToolsPckgs/Pmv
> X Error of failed request:  GLXUnsupportedPrivateRequest
>  Major opcode of failed request:  152 (GLX)
>  Minor opcode of failed request:  17 (X_GLXVendorPrivateWithReply)
>  Serial number of failed request:  780
>  Current serial number in output stream:  780
>
>  With 1.4.4 release i get it to load and work half of the time but with
> 1.4.5
> release it doesn't load past 1%.
>
>  Does anybody have a suggestion about what is causing this and how to deal
> with
> it?
>
>  Appreciate any help,
>
>  Lena
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 5 Jun 2007 23:53:32 +0300
> From: hassan shallal <hassanshallal at hotmail.com>
> Subject: Re: ADL: PMV crashes upon opening
> To: <ldolghih at gmail.com>
> Cc: autodock at scripps.edu
> Message-ID: <BAY128-W107407E710CAC23657DAA6BE200 at phx.gbl>
> Content-Type: text/plain; charset="windows-1256"
>
>
>
> Ok Elena,
>
> Make sure that the stackszie is defined unlimited in your source ~.bashrc and ~.bash_profile.
> I think the problem you have might be solved this way.
>
> Good luck
> Hassan Shallal
> University of the Pacific
> Stockton / CA
>
>
>
> ----------------------------------------
> > Date: Tue, 5 Jun 2007 15:17:57 -0400
> > From: ldolghih at gmail.com
> > To: autodock at scripps.edu
> > Subject: ADL: PMV crashes upon opening
> >
> > Hello,
> >
> > I have a problem with running PMV.
> >
> > After editing my .kshrc file following the installation instructions, I type
> > pmv
> > in the command line and can
> > see PMV window open and then crash with the following message:
> >
> >
> > linx32% pmv
> > setting PYTHONHOME environment
> > Run PMV from  /ufl/qtp/jlk/ld/MGLTools-1.4.5/MGLToolsPckgs/Pmv
> > X Error of failed request:  GLXUnsupportedPrivateRequest
> >  Major opcode of failed request:  152 (GLX)
> >  Minor opcode of failed request:  17 (X_GLXVendorPrivateWithReply)
> >  Serial number of failed request:  780
> >  Current serial number in output stream:  780
> >
> >  With 1.4.4 release i get it to load and work half of the time but with
> > 1.4.5
> > release it doesn't load past 1%.
> >
> >  Does anybody have a suggestion about what is causing this and how to deal
> > with
> > it?
> >
> >  Appreciate any help,
> >
> >  Lena
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
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>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 5 Jun 2007 17:06:47 -0500
> From: "snoze pa" <snoze.pa at gmail.com>
> Subject: ADL: Auto Gridcenter in autodock 4
> To: autodock <autodock at scripps.edu>
> Message-ID:
>        <10f848910706051506m6f4c5165j4f604ae377f8f4cc at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi, I am screening a library. but i am gettiing auto grid center in latest
> MGLtools. Since the ligands are different, so the atom names.
> Is it possible to supply the grid coordinate using command line.
>
> If you following this tutorials
>
> http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-grid-parameter-files-for-autogrid4
>
> then i can see a variable
>
> -p parameter=newvalue
>
> if i am using -p gridcenter=10.2 102.1 11.2
>
> it is giving error and not creating any more output file.
>
> Anyhelp, thanks in advance
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 5 Jun 2007 19:19:54 -0400
> From: "Jack Shultz" <jackygrahamez at gmail.com>
> Subject: ADL: AUTDOCK & BOINC
> To: autodock at scripps.edu
> Message-ID:
>        <6c65435e0706051619s793e93f5m28756121ea13e332 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
>
> I am developing a BOINC project and I noticed there are references to the
> BOINC API in Autodock4 main.cc
> Is anyone using Autodock on BOINC?
>
> Jack
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 06 Jun 2007 01:44:32 +0000
> From: "David Harrison" <david_harrison11 at hotmail.com>
> Subject: ADL: Excercise Problem
> To: autodock at scripps.edu
> Message-ID: <BAY121-F3183FF958262A0D3B05E55FC270 at phx.gbl>
> Content-Type: text/plain; format=flowed
>
> Hello,
>
> Can anyone send me the tutorial files for autodock4, the fully formated
> files? Each file from exercise 1-7.  The tutorial has the information but
> only audodock3 files.  Will be good to have files that I know work, so I can
> check if my setup is o.k.
>
> Thanks
>
> _________________________________________________________________
> Advertisement: Makeover Your Finances - WIN a $3000 Planning Package
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>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 5 Jun 2007 22:16:34 -0400
> From: "hua wang" <wanghuaa at gmail.com>
> Subject: ADL: about autodock4
> To: autodock at scripps.edu
> Message-ID:
>        <d64c44610706051916v3dd2a99fg998d0feff5d5c200 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> I have 3 ligands to run, they were good under autodock3, but 2 of them gave
> trouble, when I ran autodock4. .dlg files showed ' error, torsion number 1
> between atom 1 and 741417022 atom has more (out of 5 atoms) that are out of
> range', only one ligand works well under autodock4. Who can give me a hint
> what's wrong here?
>
> Thanks,
>
> helene
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 06 Jun 2007 10:45:26 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: ADL: Auto Gridcenter in autodock 4
> To: autodock <autodock at scripps.edu>
> Message-ID: <46661FC6.6040002 at yahoo.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Have you put quote marks around the coordinates?
>
> On 6/6/2007 6:06 AM, snoze pa wrote:
> > Hi, I am screening a library. but i am gettiing auto grid center in latest
> > MGLtools. Since the ligands are different, so the atom names.
> > Is it possible to supply the grid coordinate using command line.
> >
> > If you following this tutorials
> >
> > http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-grid-parameter-files-for-autogrid4
> >
> > then i can see a variable
> >
> > -p parameter=newvalue
> >
> > if i am using -p gridcenter=10.2 102.1 11.2
> >
> > it is giving error and not creating any more output file.
> >
> > Anyhelp, thanks in advance
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
> >
> >
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 06 Jun 2007 06:57:10 +0000
> From: "David Harrison" <david_harrison11 at hotmail.com>
> Subject: ADL: Installation Help
> To: autodock at scripps.edu
> Message-ID: <BAY121-F253515BF3D58347530EF04FC270 at phx.gbl>
> Content-Type: text/plain; format=flowed
>
> Can someone please give a clear step by step method of installing Autodock,
> MGLTools and Python on a Windows platform?
>
> >From the basic file download of all the different components to the actual
> usage of Autodock?  At the moment all this information is scattered.  I
> think if we have one clear description of how to install Autodock a lot of
> questions won't have to be repeated.
>
> Any help will be greatly appreciated.
>
> Dave
>
> _________________________________________________________________
> Advertisement: Makeover Your Finances - WIN a $3000 Planning Package
> http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Fwww%2Eletsshop%2Ecom%2FDefault%2Easpx%3Ftabid%3D948&_t=764144777&_r=letshop_emailtaglines_june07&_m=EXT
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 06 Jun 2007 09:57:28 +0200
> From: Joan Teyra <jt at biotec.tu-dresden.de>
> Subject: ADL:  pdb/dlg sorted by docked Energies
> To: autodock <autodock at scripps.edu>
> Message-ID: <466668E8.3090004 at biotec.tu-dresden.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear ADockers,
> Normally the dlg file output is sorted by docked run.
> I would like to have a PDB file containing all the docked structures
> sorted by Docked Energies.
> Is there any script around?
>
> I already know that you can get an histogram table linking clustering
> num. with run num. but still I would have to code.
> Any suggestion is really welcome.
> Thanks in advance, Joan.
>
> --
> _______________________________________________
> ***********************************************
> Joan Teyra
> Structural Bioinformatics Group
> Biotechnologisches Zentrum, TU Dresden (Germany)
>
> w?:www.biotec.tu-dresden.de/~joan
> e: joan.teyra at biotec.tu-dresden.de
> t: +49(0351)46340078
> _______________________________________________
> ***********************************************
>
>
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 39, Issue 6
> ***************************************
>


Dear all
I am working on Xeon computer but I have problem to run Autodock4,
have worked anybody in this kind of machines?.
Best wishes
Jose


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