ADL: autodock Digest, Vol 58, Issue 24

Megan Arrington megan.arrington at gmail.com
Sun Jun 21 10:09:36 PDT 2009


On Fri, Jun 19, 2009 at 9:14 PM, <autodock-request at scripps.edu> wrote:

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> Today's Topics:
>
>   1.  New candidate releases of AutoDock and AutoDockTools and new
>      User Forum (arthur olson)
>   2. Re:  New candidate releases of AutoDock and AutoDockTools and
>      new User Forum (Oleg Trott)
>   3. Re:  New candidate releases of AutoDock and AutoDockTools and
>      new User Forum (Mark Swingle)
>   4.  Problem Compiling Autogrid 5.2.1 (Stephen P. Molnar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 19 Jun 2009 13:25:00 -0700
> From: arthur olson <olson at scripps.edu>
> Subject: ADL: New candidate releases of AutoDock and AutoDockTools and
>        new User Forum
> To: autodock at scripps.edu
> Message-ID: <4A3BF41C.4040002 at scripps.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> We are pleased to announce candidate releases of AutoDock and
> AutoDockTools software, as well as a new MGL Forum. After a period of
> review and feedback from the community, official releases will be made.
>
> AutoDock 4.2.1 release candidate 1: available
> from http://autodock.scripps.edu/downloads
> Changes in AutoDock4.2:
> Improved methods for local search
> More stable model for the unbound state
> Bug fixes
>
> AutoDockTools 4.2:
> available in MGLTools 1.5.4 Release Candidate 1
> from http://mgltools.scripps.edu/downloads
> Changes in AutoDockTools (ADT):
> New default settings for creating grid and docking parameter files.
> AutoLigand automatically available
> Bug fixes
>
> MGL Forum:
> available from  http://mgl.scripps.edu/forum/
> The new forum provides our user community with an organized
> infrastructure for discussion and mutual assistance. There are different
> forum rooms for each of the MGL programs, as well as general discussions
> on docking related topics. All topics and forum threads are indexed and
> searchable.
> -----------------
>
> --
> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
>
> Arthur J. Olson, Ph.D.
> Professor
> Department of Molecular Biology
> The Scripps Research Institute
> La Jolla, CA 92037
> tel. (858) 784-9702
> fax. (858) 784-2860
> http://www.scripps.edu/pub/olson-web
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 19 Jun 2009 14:24:55 -0700
> From: Oleg Trott <trott at scripps.edu>
> Subject: Re: ADL: New candidate releases of AutoDock and AutoDockTools
>        and     new User Forum
> To: autodock at scripps.edu
> Message-ID:
>        <217ff3f30906191424w7fc6548dqf3d0239f214db88e at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Fri, Jun 19, 2009 at 1:25 PM, arthur olson<olson at scripps.edu> wrote:
>
> > MGL Forum:
> > available from ?http://mgl.scripps.edu/forum/
> > The new forum provides our user community with an organized
> infrastructure
> > for discussion and mutual assistance. There are different forum rooms for
> > each of the MGL programs, as well as general discussions on docking
> related
> > topics. All topics and forum threads are indexed and searchable.
> > -----------------
>
>
> I would like to add that the AutoDock Vina section of the MGL forum is
> the only place where I plan to continue to provide support for
> AutoDock Vina, time permitting.
>
> The focus of the forum will be, like the focus of the mailing list
> was, community support, i.e. users helping each other. So please, try
> to answer other users' questions you have an answer to. This may leave
> me more time to answer your own queries.
>
> Thanks,
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> http://olegtrott.com
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 19 Jun 2009 18:51:24 -0500
> From: Mark Swingle <mswingle at jaguar1.usouthal.edu>
> Subject: Re: ADL: New candidate releases of AutoDock and AutoDockTools
>        and new User Forum
> To: autodock at scripps.edu
> Message-ID: <200906191851.24785.mswingle at jaguar1.usouthal.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dr. Olson et al,
>
> Thanks for the new release!
>
> Is the pattern search algorithm part of the "improved methods for local
> search" in 4.2.1? I noticed that there was a section of the source code
> that
> seems to implement this, but when I try it I an get error message
>
> autodock4: ./gs.cc:630: void Genetic_Algorithm::crossover(Population&):
> Assertion `(aQOK_mag4 > 0.999) && (aQOK_mag4 < 1.001)' failed.
>
> which, I think, indicates that the quaternion is getting screwed up
> somehow.
> Was this intended to be functional in the 4.2.1 release? If not, I won't
> bother submitting a bug report.
>
> Along the same lines, I was wondering if the ga_termination keyword is
> useable
> in this release.
>
> Regards,
>
> Mark
>
>
> On Friday 19 June 2009 03:25:00 pm arthur olson wrote:
> > We are pleased to announce candidate releases of AutoDock and
> > AutoDockTools software, as well as a new MGL Forum. After a period of
> > review and feedback from the community, official releases will be made.
> >
> > AutoDock 4.2.1 release candidate 1: available
> > from http://autodock.scripps.edu/downloads
> > Changes in AutoDock4.2:
> > Improved methods for local search
> > More stable model for the unbound state
> > Bug fixes
> >
> > AutoDockTools 4.2:
> > available in MGLTools 1.5.4 Release Candidate 1
> > from http://mgltools.scripps.edu/downloads
> > Changes in AutoDockTools (ADT):
> > New default settings for creating grid and docking parameter files.
> > AutoLigand automatically available
> > Bug fixes
> >
> > MGL Forum:
> > available from  http://mgl.scripps.edu/forum/
> > The new forum provides our user community with an organized
> > infrastructure for discussion and mutual assistance. There are different
> > forum rooms for each of the MGL programs, as well as general discussions
> > on docking related topics. All topics and forum threads are indexed and
> > searchable.
> > -----------------
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 19 Jun 2009 21:14:28 -0400
> From: "Stephen P. Molnar" <s.molnar at sbcglobal.net>
> Subject: ADL: Problem Compiling Autogrid 5.2.1
> To: AutoDock <autodock at scripps.edu>
> Message-ID: <4A3C37F4.5060101 at sbcglobal.net>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> I have downloaded and partially compiles autodocksuite-4.2.1-src in my
> OpenSuSE 10.6 64bit AMD platform.  I say partially, because while
> autodock compiled without any warning or error messages, autogrid did
> not.  I have attached the configuration and make logs for autogrid.
>
> Assistance will be appreciated.
>
> Thanks in advance.
>
> --
> Stephen P. Molnar, Ph.D.
> Foundation for Chemistry
> http://www.geocities.com/FoundationForChemistry
>
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> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 58, Issue 24
> ****************************************
>


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