[Dock-fans] Dock-fans Digest, Vol 59, Issue 13

Fri Apr 17 00:29:39 PDT 2009

Hi everybody

I m adding Hydrogen to my ligand file .Actually this file contain 1990
ligand .Now while adding hydrogen ,this is givin chimera error :-
Cannot find consistent set of bond orders for ring system containing atom
#0.1881:1.het at C
Cannot find consistent set of bond orders for ring system containing atom
#0.1942:1.het at C
so on ,....................
what should i do to remove this error ? Pls reply me ...
Waiting for ur reply.....

On Thu, Apr 16, 2009 at 10:34 PM, <dock-fans-request at docking.org> wrote:

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> Today's Topics:
>
>   1. calculating binding sites volume overlap (Ben Keshet)
>   2. Re: About the "legacy_accessories" of the dock6 (CAI Qixu)
>   3. request (shalu jhanwar)
>   4. Re: About the "legacy_accessories" of the dock6 (Aurum Bai)
>   5. dock3.5.54 (Collignon, Barbara C.)
>   6. Re: dock3.5.54 (John J. Irwin)
>   7. Re: calculating binding sites volume overlap (John J. Irwin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 15 Apr 2009 16:21:42 -0400
> From: Ben Keshet <keshet1 at umbc.edu>
> Subject: [Dock-fans] calculating binding sites volume overlap
> To: dock-fans <dock-fans at docking.org>
> Message-ID: <49E641D6.8080905 at umbc.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Dock-fans,
>
> I want to calculate the degree of volume overlap of two ligands docked
> at close proximity (not at the same time). I thought of using sphgen to
> generate the positive (inside surface) representation of the ligands as
> a cluster of overlapping spheres. Then calculate the clusters volume
> (say V1 and V2), and calculate the overlapping volume of V1 with V2,
> which is the overlapping volume occupied by both ligands (separately,
> not at the same time).
>
> Does anyone know a tool that can do something like that (Dock, Chimera
> or anything else)? Does anyone know if Mathematica is suitable for that?
> The analytical solution becomes complicated when the number of spheres
> increase, so I am trying to construct some numerical method to calculate
> the overlapping volume (but I am not a programmer so it's becoming time
> consuming). Any ideas are appreciated.
>
> Thanks,
> Ben Keshet
> University of Maryland Baltimore County (UMBC)
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 16 Apr 2009 12:52:01 +0800
> From: CAI Qixu <caiqixu at gmail.com>
> Subject: Re: [Dock-fans] About the "legacy_accessories" of the dock6
> To: li bai <javacfish at yahoo.com.cn>
> Cc: dock-fans at docking.org
> Message-ID:
>        <6c9a0f510904152152t12ecc23fsba432da933e6894a at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> Could you tell me how to compile the sortDOCKout.f?
> Thank you very much.
>
> Qixu Cai
> Email: caiqixu at gmail.com
> Xiamen University, Fujian, China
>
>
> On Mon, Apr 13, 2009 at 10:52 AM, li bai <javacfish at yahoo.com.cn> wrote:
>
> >  Hello,everyone!
> >
> > I am happy to write another letter to disscuss the function of
> > legacy_accessories. I compile the legacy_accessories and found the
> >  "sortDOCKout" script.
> >
> > ./sortDOCKout --help, it is err
> >
> > How do I use "sortDOCKout"? What is founction ?
> >
> > Thanks
> > Aurum
> >
> >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
> >
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> ------------------------------
>
> Message: 3
> Date: Thu, 16 Apr 2009 14:05:43 +0530
> From: shalu jhanwar <shalu.jhanwar17 at gmail.com>
> Subject: [Dock-fans] request
> To: dock-fans at docking.org
> Message-ID:
>        <411c5dfb0904160135r56ea752n2ae07a9e5b1b51b7 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everybody
>
> I hv done docking by taking single molecule(ligand) .Bt now i hv to do
> virtual screening .Can anyone tell that what precautions i should take ?
>
> Thanking you .
> waiting for ur replies......
> --
> Shalu Jhanwar
> M.Sc Bioinformatics
> Banasthali University
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> ------------------------------
>
> Message: 4
> Date: Thu, 16 Apr 2009 18:55:44 +0800 (CST)
> From: Aurum Bai <javacfish at yahoo.com.cn>
> Subject: Re: [Dock-fans] About the "legacy_accessories" of the dock6
> To: CAI Qixu <caiqixu at gmail.com>
> Cc: dock-fans at docking.org
> Message-ID: <456930.39205.qm at web15006.mail.cnb.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> Your GCC compoler must be 3.X, not the 4.x, and you must write the Makefile
> by yourself.
> In addtions, Gcc compiler must contain the f77.
> ?
> Good luck
> ?
> Aurum
>
> --- On Thu, 4/16/09, CAI Qixu <caiqixu at gmail.com> wrote:
>
>
> From: CAI Qixu <caiqixu at gmail.com>
> Subject: Re: [Dock-fans] About the "legacy_accessories" of the dock6
> To: "li bai" <javacfish at yahoo.com.cn>
> Cc: dock-fans at docking.org
> Date: Thursday, April 16, 2009, 12:52 PM
>
>
> Hi,
> Could you tell me how to compile the sortDOCKout.f?
> Thank you very much.
>
> Qixu Cai
> Email: caiqixu at gmail.com
> Xiamen University, Fujian, China
>
>
>
> On Mon, Apr 13, 2009 at 10:52 AM, li bai <javacfish at yahoo.com.cn> wrote:
>
>
>
>
>
>
> Hello,everyone!
> ?
> I am happy to write another letter to disscuss the function of
> legacy_accessories. I compile the legacy_accessories and found?the
> ?"sortDOCKout" script.
> ?
> ./sortDOCKout --help, it is err
> ?
> How do I use "sortDOCKout"? What is founction ?
> ?
> Thanks
> Aurum
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
>
>
>
>
>
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> ------------------------------
>
> Message: 5
> Date: Thu, 16 Apr 2009 12:09:09 -0400
> From: "Collignon, Barbara C." <collignonbc at ornl.gov>
> Subject: [Dock-fans] dock3.5.54
> To: dock-fans at docking.org
> Message-ID:
>        <E970EE66714B5741A9CF3C407B860578087DBB31 at ORNLEXCHANGE.ornl.gov>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi everybody,
>
>
> I use dock6.2.
>
> Is the anchor-and-grow algorithm implemented in dock3.5.54 ?
>
> Barbara
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 16 Apr 2009 09:44:27 -0700
> From: "John J. Irwin" <jji at cgl.ucsf.edu>
> Subject: Re: [Dock-fans] dock3.5.54
> To: "Collignon, Barbara C." <collignonbc at ornl.gov>
> Cc: dock-fans at docking.org
> Message-ID: <49E7606B.9040500 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Barbara
>
> Here are the references that explain how DOCK 3.5.54 works:
>
> Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple
> ligand conformations. /Curr Top Med Chem/* 5* (8), 739-49 (2005).
> [Pubmed
> <
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16101414&query_hl=1&itool=pubmed_docsum>
> | Download
> PDF <http://shoichetlab.compbio.ucsf.edu/publications/lorber_reprint.pdf>]
>
> Lorber DM, Shoichet BK. Flexible ligand docking using conformational
> ensembles. /Protein Science/* 7*, 938-950 (1998). [Pubmed
> <
> http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9568900&dopt=Abstract>
> | DOI
> <http://dx.doi.org/10.1021/jm980343w>]
>
> as cited on the web page
> http://shoichetlab.compbio.ucsf.edu/publications.php
>
> In short, we do not use anchor-and-grow as in DOCK 4, but we enumerate
> conformations in advance and dock them all at once, as an ensemble, and
> then prune the tree to find the best pose.  This is the only way we have
> found to be able to sample 10^6 implied conformations in under one cpu
> second.
>
> Good docking!
>
> John
> UCSF DOCK Team
>
>
> Collignon, Barbara C. wrote:
> > Hi everybody,
> >
> >
> > I use dock6.2.
> >
> > Is the anchor-and-grow algorithm implemented in dock3.5.54 ?
> >
> > Barbara
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
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> ------------------------------
>
> Message: 7
> Date: Thu, 16 Apr 2009 10:02:45 -0700
> From: "John J. Irwin" <jji at cgl.ucsf.edu>
> Subject: Re: [Dock-fans] calculating binding sites volume overlap
> To: Ben Keshet <keshet1 at umbc.edu>
> Cc: dock-fans <dock-fans at docking.org>
> Message-ID: <49E764B5.4000803 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Ben
> <http://xray.bmc.uu.se/usf/ligcom_man.html>
> I saw this paper, but I don't know whether this idea is available is
> free, ready-to-go software: **J Chem Inf Model. <javascript:AL_get(this,
> 'jour', 'J Chem Inf Model.');> 2008 Jul;48(7):1411-22. Epub 2008 Jul 4.
>  An Alternative method for the evaluation of docking performance: RSR vs
> RMSD. by *Yusuf D*
> </sites/entrez?Db=pubmed&Cmd=Search&Term=%22Yusuf%20D%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>,
> *Davis
> AM*
> </sites/entrez?Db=pubmed&Cmd=Search&Term=%22Davis%20AM%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>,
> *Kleywegt
> GJ*
> </sites/entrez?Db=pubmed&Cmd=Search&Term=%22Kleywegt%20GJ%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>,
> *Schmitt
> S*
>
> </sites/entrez?Db=pubmed&Cmd=Search&Term=%22Schmitt%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>.
>
> *
> *There is also a program Ligcom that looks close-ish:
> http://xray.bmc.uu.se/usf/ligcom_man.html.
> <http://xray.bmc.uu.se/usf/ligcom_man.html>
>
> It also should be fairly straightforwared to do this with EON from Openeye.
>
> Hope this is some use.
>
> Good docking
>
> John
> UCSF DOCK Team
>
>
> Ben Keshet wrote:
> > Hi Dock-fans,
> >
> > I want to calculate the degree of volume overlap of two ligands docked
> > at close proximity (not at the same time). I thought of using sphgen to
> > generate the positive (inside surface) representation of the ligands as
> > a cluster of overlapping spheres. Then calculate the clusters volume
> > (say V1 and V2), and calculate the overlapping volume of V1 with V2,
> > which is the overlapping volume occupied by both ligands (separately,
> > not at the same time).
> >
> > Does anyone know a tool that can do something like that (Dock, Chimera
> > or anything else)? Does anyone know if Mathematica is suitable for that?
> > The analytical solution becomes complicated when the number of spheres
> > increase, so I am trying to construct some numerical method to calculate
> > the overlapping volume (but I am not a programmer so it's becoming time
> > consuming). Any ideas are appreciated.
> >
> > Thanks,
> > Ben Keshet
> > University of Maryland Baltimore County (UMBC)
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
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> ------------------------------
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
>
> End of Dock-fans Digest, Vol 59, Issue 13
> *****************************************
>

-- 
Shalu Jhanwar
M.Sc Bioinformatics
Banasthali University
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