ADL: autodock Digest, Vol 53, Issue 26

jose correa corrjose at gmail.com
Fri Jan 23 12:22:28 PST 2009


Hi,
I would be very thankful if someone gives me more information about how can
i visualize the interactions between the best conformation obtained by
docking and the macromolecule. Also i would know if i can extract a file
with the residues that are interacting. Does exist any bioinformatic
software available for that purpose?
Regards,
Isabel Hilliger

Dear Isabel
You can do these by using Autodock Tools, if you want to see more
atomic details, you can take the ligand-protein complex coordenates and use
the VMD.
I hope it helps you
J Correa-Basurto
ESM-IPN, Mexico

2009/1/23 <autodock-request at scripps.edu>

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> Today's Topics:
>
>   1.  Missing parameters for the transition metal atoms in
>      AutoDock (Huang Zunnan)
>   2. Re:  autodock Digest, Vol 53, Issue 25 (Isabel Hilligerk)
>   3.  Question on AutoDock platform support (John Gorski)
>   4.  (no subject) (Bolser, Diana Katherine (MU-Student))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 22 Jan 2009 16:04:16 -0800 (PST)
> From: Huang Zunnan <zunnanh at yahoo.com>
> Subject: ADL: Missing parameters for the transition metal atoms in
>        AutoDock
> To: autodock at scripps.edu
> Message-ID: <88785.28056.qm at web45112.mail.sp1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear all:
> ?
> I plan to perform a virtual screen of a bacteria protein againt?the?NCI
> diversity set. I need the energy?parameters of the transtion?metal atoms in
> order to generate?their grid map file.?I donot know how to?get?the?energy
> parameters accurately for those transiton metal atoms.?Any
> suggestions?greatly appreciated!
> ?
> Best Regards
> Zunnan H.
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 23 Jan 2009 13:05:12 -0300
> From: Isabel Hilligerk <isabel.hilligerk at gmail.com>
> Subject: Re: ADL: autodock Digest, Vol 53, Issue 25
> To: autodock at scripps.edu
> Message-ID:
>        <9ede39d40901230805v2bd12862je95d35caa32e7e66 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> I would be very thankful if someone gives me more information about how can
> i visualize the interactions between the best conformation obtained by
> docking and the macromolecule. Also i would know if i can extract a file
> with the residues that are interacting. Does exist any bioinformatic
> software available for that purpose?
> Regards,
> Isabel Hilliger
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 23 Jan 2009 09:31:03 -0600
> From: "John Gorski" <jgorski at sgi.com>
> Subject: ADL: Question on AutoDock platform support
> To: <autodock at scripps.edu>
> Message-ID:
>        <
> 1AB9A794DBDDF54A8A81BE2296F7BDFE51A11C at cf--amer001e--3.americas.sgi.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
>
>
> I have a question for you regarding AutoDock4. I was looking at your
> website and could not find the answer.
>
>
>
> It says the application is supported on Linux. But is this the x86_64
> version of Linux or is it 32bit version?
>
>
>
> I am guessing since it runs on IRIX and MACos it is 64bit but would like
> to confirm the Linux version.
>
>
>
> Thanks
>
>
>
> John
>
>
>
> ..............................
>
>
>
> John Gorski
>
> Systems Engineer
>
> SGI
>
>
>
> jgorski at sgi.com
>
> tel: 703.608.3229
>
> fax: 301.572.3280
>
> sgi.com
>
>
>
>
>
>  ..............................
>
> Why is the man who invests all your money called a broker?
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 23 Jan 2009 12:57:35 -0600
> From: "Bolser, Diana Katherine (MU-Student)" <dkbc59 at mizzou.edu>
> Subject: ADL: (no subject)
> To: <autodock at scripps.edu>
> Message-ID:
>        <DEEED37DD7C63D42B65D4DE9473AD7A2599AC1 at UM-XMAIL01.um.umsystem.edu>
> Content-Type: text/plain;       charset="iso-8859-1"
>
> I need autodock to generate 500 conformations, so I set the ga_run
> parameter to 500. In the .dlg file, it said I needed to edit the source file
> called constants.h. I noticed in the faq's section of the website a path was
> provided to the constants.h file, however, none of my files match the path.
> Where do I find constants.h?
>
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 53, Issue 26
> ****************************************
>



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