ADL: autodock Digest, Vol 43, Issue 24

jose correa corrjose at gmail.com
Fri Oct 19 12:21:41 PDT 2007


Dear Tim
You must check the *.dlg with a text editor. Maybe there is not any
simulation and you should sent the docking simulations again.
Best wishes
Jose Correa


2007/10/19, autodock-request at scripps.edu <autodock-request at scripps.edu>:
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> Today's Topics:
>
>   1. Re:  ADT failed to open dlg file (Tim Zhang)
>   2.  How to get the XYZ coordinates information? (IVYtony smth)
>   3. Re:  ADT failed to open dlg file (Paola Beassoni)
>   4. Re:  How to get the XYZ coordinates information?
>      (german at my-elcot.de)
>   5.  dlg file not generated in SA (Ana Margarida)
>   6. Re:  Autodock 4 (Yang Ye)
>   7. Re:  About Problem of Autodock4, thanks! (snoze pa)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 18 Oct 2007 13:14:56 -0700 (PDT)
> From: Tim Zhang <haomingz at yahoo.com>
> Subject: Re: ADL: ADT failed to open dlg file
> To: autodock at scripps.edu
> Message-ID: <942070.54453.qm at web63404.mail.re1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi,
>
> I can't open dlg file after docking a ligand to macromolecules using
> autodock4 and would appreciate help from you. I checked the dlg file and it
> shows the docking is successful and I can see the coordinates. But when I
> use ADT to analyze the docking, no conformations were loaded to ADT. I
> wonder if anyone has a solution for this. Thank you!!
>
> Tim
>
> __________________________________________________
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> ------------------------------
>
> Message: 2
> Date: Thu, 18 Oct 2007 15:35:16 -0600
> From: "IVYtony smth" <ivytony at gmail.com>
> Subject: ADL: How to get the XYZ coordinates information?
> To: autodock at scripps.edu
> Message-ID:
>        <b290f3e30710181435u1f5b6679o4de46558aab3ad6f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I am just wondering how to determine the XYZ coordinates information if I
> know the binding site on a protein surface?
>
> thanks!
>
> --
> Signature: Success is a journey that never ends.
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 18 Oct 2007 20:17:42 -0300
> From: "Paola Beassoni" <paobeassoni at gmail.com>
> Subject: Re: ADL: ADT failed to open dlg file
> To: autodock at scripps.edu
> Message-ID:
>        <579b6a5b0710181617o5fd0380ct92d4f2cf3742cb4f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Tim,
> send us the dlg generated file so we can chek it out! I will try to
> analyze it!
> Best regads
> Paola
>
>
> 2007/10/18, Tim Zhang <haomingz at yahoo.com>:
> > Hi,
> >
> > I can't open dlg file after docking a ligand to macromolecules using
> autodock4 and would appreciate help from you. I checked the dlg file and it
> shows the docking is successful and I can see the coordinates. But when I
> use ADT to analyze the docking, no conformations were loaded to ADT. I
> wonder if anyone has a solution for this. Thank you!!
> >
> > Tim
> >
> >  __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam protection around
> > http://mail.yahoo.com
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
> --
> Paola Beassoni - PhD
> Dpto. Biologia Molecular - FCEFQyN
> Universidad Nacional de Rio Cuarto
> R?o Cuarto - Argentina
> 00-54-358-4676422
> 00-54-358-4676232 (Fax)
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 19 Oct 2007 07:13:51 +0200 (CEST)
> From: german at my-elcot.de
> Subject: Re: ADL: How to get the XYZ coordinates information?
> To: autodock at scripps.edu
> Message-ID:
>        <37366.195.145.28.238.1192770831.squirrel at ssl.puettmann.net>
> Content-Type: text/plain;charset=iso-8859-1
>
> > I am just wondering how to determine the XYZ coordinates information if
> I
> > know the binding site on a protein surface?
> >
> > thanks!
>
> If you know the binding site than you can check the cooridnates of one
> atom near the binding site in MOE or SYBYL, and center the grid box on
> these coordinates
>
> Bye,
>
> German
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 2 Oct 2007 10:47:45 +0100
> From: "Ana Margarida" <amdr33 at hotmail.com>
> Subject: ADL: dlg file not generated in SA
> To: <autodock at scripps.edu>
> Message-ID: <BAY106-DAV1F2BD60C3600AA6B989AED59F0 at phx.gbl>
> Content-Type: text/plain;       charset="iso-8859-1"
>
> Hi everyone,
>
> I've sent this e-mail before, but i didn't notice that de pc date and time
> were wrong, so it is in 2002.. Sorry...
>
> I've came up with a problem while trying to use SA instead of GA... It
> seems that my autodock job dies at the same time that it starts! The
> autogrid4 calculations were done with no problem but the autodock fails...
> As i?m starting i decided to use the default parameters of autodock SA. Does
> anyone have a possible solution or an ideia of the problem?
>
> Thanks
>
> Ana Margarida
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 19 Oct 2007 18:16:39 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: ADL: Autodock 4
> To: IVYtony smth <ivytony at gmail.com>, autodock <autodock at scripps.edu>
> Message-ID: <47188407.7010205 at yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> The analysis says that each result forms a cluster; there is no cluster
> found.
>
> As I wrote before, docking a 20 peptide dock is a too ambitious move.
> The large negative energy shown is too bizaare for reasonable result. I
> doubt in the approach.
>
> To retrieve structure from dlg file, I found Ad3's utility helpful. I
> attach get-docked script here.
>
> Regards,
> Yang Ye
>
> On 10/19/2007 6:47 AM, IVYtony smth wrote:
> > Hi Yang Ye,
> >
> > This is Tony Wang. I am the guy who posted a question regarding
> > docking a 20aa peptide onto a protein. I do find the "Histogram" in my
> > dlg file as follows. However, how do I interprete this diagram? and
> > How can I visualize the best docked conformation?
> >
> > Thanks a million!
> >
> > Tony
> >
> >     CLUSTERING HISTOGRAM
> >     ____________________
> >
> >
> ________________________________________________________________________________
> >      |           |     |           |
> > |
> > Clus | Lowest    | Run | Mean      | Num |
> > Histogram
> > -ter | Binding   |     | Binding   | in
> > |
> > Rank | Energy    |     | Energy    | Clus|    5    10   15   20   25
> > 30   35
> >
> _____|___________|_____|___________|_____|____:____|____:____|____:____|____:___
> >    1 |-12423570391040.00 |   4 |-12423570391040.00 |   1 |#
> >    2 |-11923820118016.00 |   1 |-11923820118016.00 |   1 |#
> >    3 |- 11670521905152.00 |   9 |-11670521905152.00 |   1 |#
> >    4 |-11182784118784.00 |   5 |-11182784118784.00 |   1 |#
> >    5 |-11123252264960.00 |   8 |-11123252264960.00 |   1 |#
> >    6 |-9930319855616.00 |  10 |-9930319855616.00 |   1 |#
> >    7 |-9547153408000.00 |   2 |-9547153408000.00 |   1 |#
> >    8 |-8967887519744.00 |   7 |-8967887519744.00 |   1 |#
> >    9 |-8629512568832.00 |   6 |-8629512568832.00 |   1 |#
> >   10 |-3623251869696.00 |   3 |- 3623251869696.00 |   1 |#
> >
> _____|___________|_____|___________|_____|______________________________________
> >
> > --
> > Signature: Success is a journey that never ends.
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> ------------------------------
>
> Message: 7
> Date: Fri, 19 Oct 2007 11:23:19 -0500
> From: "snoze pa" <snoze.pa at gmail.com>
> Subject: Re: ADL: About Problem of Autodock4, thanks!
> To: autodock at scripps.edu
> Message-ID:
>        <10f848910710190923n47234d78he3d4a799235ea52f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I am unable to get any information where and when autodock uses the
> receptor_flex.pdbqt file. Because both dpf and gpf file don't have any
> information related to flexible residues though i have created one. Then
> how
> they can use this file to process the flexible residue based docking. Are
> you sure that you have receptor_flex.pdbqt  file name in your dpf or gpf
> files. If yes please let me know. I posted this question few days back but
> didn't get any reply from anyone. I also check the example tutorial in ADT
> new version. Though the flexible residue files name are there but not in
> neither in gpf nor in dpf files. That will be a great help. thanks
>
> On 10/17/07, mswingle at jaguar1.usouthal.edu <mswingle at jaguar1.usouthal.edu>
> wrote:
> >
> > I believe you need to download release 4.0.1. I had this same problem
> with
> > the first release
> > of autodock4 (release 4.0.0). This happens because autodock4 combines
> the
> > information
> > from ligand.pdbqt and receptor_flex.pdbqt together during the run.
> > Autodock4 is supposed
> > to renumber the atoms in receptor_flex.pdbqt to follow, in sequence, the
> > last atom of
> > ligand.pdbqt. However, version 4.0.0 has a bug that prevents this
> > renumbering. Version
> > 4.0.1 should work. You could also manually fix the receptor_flex.pdbqt
> > file by renumbering
> > the atoms to follow the last atom of ligand.pdbqt. That is, if, for
> > example, the last atom in
> > ligand.pdbqt is 15, then the first atom in receptor_flex.pdbqt should be
> > 16.
> >
> > Also, after fixing the numbering problem, if you get an error message
> > about "nested
> > branches", you need to upgrade AutoDockTools.
> >
> > Regards,
> >
> > Mark
> >
> > ----- Original Message -----
> > From: ggootc <ggootc at 163.com>
> > Date: Wednesday, October 17, 2007 3:18 pm
> > Subject: ADL: About Problem of Autodock4, thanks!
> > To: autodock at scripps.edu
> >
> >
> > > Dear group of autodock:
> > >    I am a chinese student in use the autodock4.0, the software is good
> > > for me but Ihave found a problem that I can't solve it, please give me
> > > some help, thank!
> > >    I have used ADT to generate the input file that include 5
> > > files"receptor_rigid.pdbqt, receptor_flex.pdbqt,  ligand.pdbqr,
> > > grid.gdf and par.gpf". WhenI use the flex_docking method to dock a
> > > small molecule to receptor in the VMware5.5environment (Red Hat
> > > Enterprise linux 4U4), the log file reports error "ATOM and
> > > HTMATMrecords must be numbered sequentially from 1" after  the line
> > > "Number of atoms inmovable ligand = 14". By check the problem, I have
> > > found that when I remove the line of"flexres receptor_flex.pdbqt #
> > > file containing flexible residues" in par.dpf, thesoftwate could be
> > > runing correctly.
> > >    How can I do it? The attachment is my 5 input files. Thanks!
> > > Sincerely: Peng ZhouDepartment of Chemistry, Zhejiang University.
> > > ________________________________________________--- ADL: AutoDock
> > List  ---  ---
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
> ------------------------------
>
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> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 43, Issue 24
> ****************************************
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