[Dock-fans] Dock-fans Digest, Vol 45, Issue 9

Syed Tarique Moin tarisyed at yahoo.com
Thu Feb 28 20:59:07 PST 2008


Hello,

Can any one guide me that which & How ZAP module
should be compiled in suse 10.2 64 bit with DOCK 6.1.

Regards 


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> Today's Topics:
> 
>    1. Re: dock installation (Scott Brozell)
>    2. i need help (do ngoc mai)
>    3. Re: i need help (Sudipto Mukherjee)
>    4. Chimera, how to prepare protein for docking
> (do ngoc mai)
>    5. flex fails to score (Francesco Pietra)
>    6. dock6 anion false hits (Hong Liang)
>    7. Re: dock6 anion false hits (John J. Irwin)
>    8. Re: Chimera, how to prepare protein for
> docking (Eric Pettersen)
> 
> 
>
----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 22 Feb 2008 14:37:57 -0800 (PST)
> From: Scott Brozell <sbrozell at scripps.edu>
> Subject: Re: [Dock-fans] dock installation
> To: Syed Tarique Moin <tarisyed at yahoo.com>
> Cc: dock-fans at docking.org
> Message-ID:
> 
>
<Pine.LNX.4.44.0802221358160.17992-100000 at bohr.scripps.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> Hi,
> 
> On Fri, 22 Feb 2008, Syed Tarique Moin wrote:
> 
> >  I want to install dock6.1, I have the intel
> fortran
> >  compile and i am using suse 10.2 64 bit. 
> 
> The simple approach is to install dock using g77.
> Unfortunately, this is not as easy as it should be
> because
> g77 is no longer distributed by default by most OSs.
> 
> >  I made change in the gnu script at this stage 
> >  FC = ifort, 
> >  then i run ./configure gnu, then i give the
> command 
> >  make all and the output is attached here.
> 
> ifort is a poor choice for one unexperienced with
> unix.
> Try gfortran instead; this is probably distributed
> with suse,
> should be easy to install if its not, and accepts
> most
> of g77's options.
> 
> >  Kindly give me suggestion.
> 
> Read this classic book or its equivalent to learn
> unix:
> 
> http://cm.bell-labs.com/cm/cs/upe/
> 
> >   > > Starting installation of DOCK v6.1
> > > ifort -O2 -fno-automatic -fno-second-underscore
> -o showbox showbox.o
> > > ifort: command line warning #10006: ignoring
> unknown
> > > option '-fno-automatic'
> 
> This is a big clue that merely changing the compiler
> is insufficent.
> One also needs to change FFLAGS.
> 
> > > grid.o: In function `main':
> > > grid.c:(.text+0x70): multiple definition of
> `main'
> > > ld: Warning: size of symbol `main' changed from
> 56
> > > in /opt/intel/fce/10.1.012/lib/for_main.o to
> 1702 in grid.o
> > > /opt/intel/fce/10.1.012/lib/for_main.o: In
> function `main':
> > > undefined reference to `MAIN__'
> > > make[2]: *** [grid] Error 1
> 
> This is already a faq:
> http://dock.compbio.ucsf.edu/DOCK_6/faq.htm
> 
> Surprisingly, searching the dock fans archives does
> not find
> a post dealing with this issue.  But now it will.
> http://dock.compbio.ucsf.edu/DOCK_6/index.htm
> 
> Scott
> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Sun, 24 Feb 2008 05:16:00 -0800 (PST)
> From: do ngoc mai <dnmai_1986 at yahoo.com>
> Subject: [Dock-fans] i need help
> To: dock-fans at docking.org
> Message-ID:
> <951005.38143.qm at web55609.mail.re4.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> i installed DMS, but i can not use it. 
> The error messages referred to radii directory, and
> i don't know how to solve this problem.
> 
> 
>   Bruindaisuki
>        
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> ------------------------------
> 
> Message: 3
> Date: Mon, 25 Feb 2008 09:46:33 -0800 (PST)
> From: Sudipto Mukherjee <sudmukh at yahoo.com>
> Subject: Re: [Dock-fans] i need help
> To: do ngoc mai <dnmai_1986 at yahoo.com>,
> dock-fans at docking.org
> Message-ID:
> <720755.16362.qm at web36702.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear do ngoc mai,
> 
> Sample radii are provided in the radii.proto file in
> the DMS installation directory.
> Use 'cp radii.proto radii' to use these radii.
> Alternatively, you can specify your own radii using
> the same format.
> 
> Regards
> Sudipto Mukherjee
> 
> 
> 
> 
> ----- Original Message ----
> From: do ngoc mai <dnmai_1986 at yahoo.com>
> To: dock-fans at docking.org
> Sent: Sunday, February 24, 2008 8:16:00 AM
> Subject: [Dock-fans] i need help
> 
> 
> i installed DMS, but i can not use it. 
> The error messages referred to radii directory, and
> i don't know how to solve this problem.
> 
> 
>   Bruindaisuki 
>       
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.
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> ------------------------------
> 
> Message: 4
> Date: Wed, 27 Feb 2008 01:54:02 -0800 (PST)
> From: do ngoc mai <dnmai_1986 at yahoo.com>
> Subject: [Dock-fans] Chimera, how to prepare protein
> for docking
> To: dock-fans at docking.org
> Message-ID:
> <208710.59266.qm at web55603.mail.re4.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> I'm preparing the protein 1SC7 for docking, but
> there're some problems when i use the Dock prep
> tool, here's the log, i don't know how to fix it
> AttributeError Exception in Tk callback
>   Function: <function command at 0x0F1EA830> (type:
> <type 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "C:\Program
>
Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py",
> line 1747, in __call__
>     return apply(self.func, args)
>   File "C:\Program
> Files\Chimera\share\chimera\baseDialog.py", line
> 238, in command
>     getattr(s, buttonFuncName(txt))()
>   File "C:\Program
> Files\Chimera\share\chimera\baseDialog.py", line
> 452, in OK
>     self.Apply()
>   File "C:\Program Files\Chimera\share\AddH\gui.py",
> line 245, in Apply
>     hisScheme=hisScheme, okCB=self.cb)
>   File "C:\Program
> Files\Chimera\share\AddH\unknownsGUI.py", line 272,
> in initiateAddHyd
>     okCB()
>   File "C:\Program
> Files\Chimera\share\DockPrep\__init__.py", line 163,
> in <lambda>
>     cb=lambda mols=mols: _postAddPrep(mols, **kw))
>   File "C:\Program
> Files\Chimera\share\DockPrep\__init__.py", line 173,
> in _postAddPrep
>     cb=lambda ur, uc, m=mols, kw=kw:
>   File "C:\Program
> Files\Chimera\share\AddCharge\__init__.py", line
> 109, in initiateAddCharges
>     nogui=nogui)
>   File "C:\Program
> Files\Chimera\share\AddCharge\__init__.py", line
> 258, in addStandardCharges
>     if pa.name == 'CA':
> AttributeError: 'NoneType' object has no attribute
> 'name'
> any suggestions?
> 
>        
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> ------------------------------
> 
> Message: 5
> Date: Wed, 27 Feb 2008 14:18:05 -0800 (PST)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: [Dock-fans] flex fails to score
> To: dock-fans <dock-fans at docking.org>
> Message-ID:
> <269013.89141.qm at web57610.mail.re1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> I am trying with DOCK6.1 to circumvent the issue of
> memory requirement at the
> ZN6Orient12match step by reducing grid and box.
> 
> Thus, with 16GB RAM available and fully usable, I
> got rigid_scored.mol2, while
> flex_scored.mol2 is zero byte without any error
> message. max_orientations was
> increased to 2000. Anchor_and_grow.out ended with:
> 
> Initializing Library File Routines...
> Initializing Orienting Routines...
> Initializing Conformer Generator Routines...
> Initializing Grid Score Routines...
>  Reading the energy grid from
> /home/francesco/dockwork/grid.nrg
> 
> 1 Molecules Processed
> Total elapsed time:	3941 seconds
> 
> while anchor_and_grow.out.1 (and all other ones for
> the other CPUs) end with;
> 
> Initializing Library File Routines...
> Initializing Orienting Routines...
> Initializing Conformer Generator Routines...
> Initializing Grid Score Routines...
>  Reading the energy grid from
>
/home/francesco/dockwork/ctx1b_WAT23_dock_box8/grid.nrg
> DOCK is currently running on deb64
> 
> 
> 0 Molecules Processed
> Total elapsed time:	0 seconds
> 
> During the computation, a max of 45% memory was
> used.
> 
> Why no error message?
> Thanks
> 
> francesco pietra
> 
> 
>      
>
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> 
> ------------------------------
> 
> Message: 6
> Date: Wed, 27 Feb 2008 23:05:10 -0700
> From: "Hong Liang" <hongliang.dal at gmail.com>
> Subject: [Dock-fans] dock6 anion false hits
> To: dock-fans at docking.org
> Message-ID:
> 
>
<510ca0cf0802272205y79767a3uab2bba93cfddd0cf at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Dock Fans,
> 
> I do not understand why Dock6 gave me so many anion
> hits: false hits.
> 
> I prepared the acceptor from sybyl 7.3 (adding
> hydrogens, applied
> kollman_all charge, manually modified the HIS around
> binding site to their
> neutral state.)  I can not see any  positive charged
>  residues  around the
> binding site.  After I docked NCI  compounds 
> downloaded  from ZINC website,
> most of compounds in the top 500 hits are anions.  
> Based on the biology
> test results of some of the anion hits,  those hits
> are false ones.
> 
> The acceptor prepared by Chimera "Dock Prep" tool
> gave similar docking
> result: most of hits are anions.  Did I miss
> something when I prepared my
> grid?  Any feedback is appreciate.
> 
> Thanks,
> 
> Hong Liang
> University of Manitoba
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> ------------------------------
> 
> Message: 7
> Date: Thu, 28 Feb 2008 11:33:42 -0800
> From: "John J. Irwin" <jji at cgl.ucsf.edu>
> Subject: Re: [Dock-fans] dock6 anion false hits
> To: Hong Liang <hongliang.dal at gmail.com>
> Cc: dock-fans at docking.org
> Message-ID: <47C70C96.7010705 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
> 
> Hi Hong
> 
> Here's what you can always do, for any binding site.
> 
> 1. Do you have any positive or negative controls? If
> so, can you 
> recapituate what you already know with your docking
> model?
> 
> 2. What is the net charge in the binding site? On
> the whole protein? 
> What is the value of the electrostatic potential
> grid in the binding 
> site? Scan you get an atomic decomposition of the
> score to investigate 
> how the molecule got the score it did? Do all the
> scores (at the atomic 
> level) look sensible?
> 
> Well, there's more, but this should get you started.
> Your motto could be 
> "Trust nothing, verify everything".
> 
> Good luck!
> 
> John
> 
> 
> Hong Liang wrote:
> > Hi Dock Fans,
> >
> > I do not understand why Dock6 gave me so many
> anion hits: false hits.
> >
> > I prepared the acceptor from sybyl 7.3 (adding
> hydrogens, applied 
> > kollman_all charge, manually modified the HIS
> around binding site to 
> > their  neutral state.)  I can not see any 
> positive charged  residues  
> > around the binding site.  After I docked NCI 
> compounds  downloaded  
> > from ZINC website, most of compounds in the top
> 500 hits are anions.   
> > Based on the biology test results of some of the
> anion hits,  those 
> > hits are false ones.
> >
> > The acceptor prepared by Chimera "Dock Prep" tool
> gave similar docking 
> > result: most of hits are anions.  Did I miss
> something when I prepared 
> > my grid?  Any feedback is appreciate.
> >
> > Thanks,
> >
> > Hong Liang
> > University of Manitoba
> >
>
------------------------------------------------------------------------
> >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> >
>
http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >   
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Thu, 28 Feb 2008 11:37:41 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Dock-fans] Chimera, how to prepare
> protein for docking
> To: dock-fans at docking.org
> Message-ID:
> <5062F4DC-D851-4120-9FC4-5BCB7AF83B0C at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> 	It is sort of a bug in Chimera.  Chimera isn't
> identifying the DT  
> bonded to PTR as a nucleic acid because the O3' is
> missing (eaten by  
> the PTR).  I have fixed this in the Chimera code and
> you can get a  
> fixed version tomorrow by going to the Chimera home
> page  
> (www.cgl.ucsf.edu/chimera) and following the "Daily
> Builds" link.
> 
> --Eric
> 
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu
> 
> 
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> End of Dock-fans Digest, Vol 45, Issue 9
> ****************************************
> 



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