ADL: autodock Digest, Vol 56, Issue 1

jose correa corrjose at gmail.com
Wed Apr 1 10:33:22 PDT 2009


ishwar chandra wrote:
> Hello Autodockers greetings
> is there any option for  mutating the protein in Autodock . If some one
> knows please reply.
> Thank You.
> Ishwar
> ________________________________________________

Dear Ishwar
Other program used for mutating is pymol: http://pymol.sourceforge.net/
best wishes
j correa-basurto
2009/4/1 <autodock-request at scripps.edu>

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> Today's Topics:
>
>   1. Re:  How to mutate the protein (Balazs JOJART)
>   2. Re:  How to mutate the protein (ishwar chandra)
>   3. Re:  How to mutate the protein (Balazs JOJART)
>   4. Re:  [gmx-users] Prepping Docking Complexes (Jack Shultz)
>   5.  Grid co-ordinates!!! (raghu bhagavat)
>   6.  Autodock problem for Grid generation (Haipeng hU)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 01 Apr 2009 09:06:41 +0200
> From: Balazs JOJART <jojartb at pharm.u-szeged.hu>
> Subject: Re: ADL: How to mutate the protein
> To: autodock at scripps.edu
> Message-ID: <49D31281.8090303 at pharm.u-szeged.hu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello Ishwar,
> In vmd you can do the mutation.
> Hope this helps,
> Balazs
>
> ishwar chandra wrote:
> > Hello Autodockers greetings
> > is there any option for  mutating the protein in Autodock . If some one
> > knows please reply.
> > Thank You.
> > Ishwar
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 1 Apr 2009 12:58:41 +0530
> From: ishwar chandra <ramramic at gmail.com>
> Subject: Re: ADL: How to mutate the protein
> To: autodock at scripps.edu
> Message-ID:
>        <c07c65cb0904010028n175d7b8an4155c73b9ff64aa0 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks but please tell VMD is an option in ADT & can we do it using GUI of
> the ADT .
> Please tell the options  / Procedure.
> Thanks again
> On Wed, Apr 1, 2009 at 12:36 PM, Balazs JOJART <jojartb at pharm.u-szeged.hu
> >wrote:
>
> > Hello Ishwar,
> > In vmd you can do the mutation.
> > Hope this helps,
> > Balazs
> >
> >
> > ishwar chandra wrote:
> >
> >> Hello Autodockers greetings
> >> is there any option for  mutating the protein in Autodock . If some one
> >> knows please reply.
> >> Thank You.
> >> Ishwar
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> >>
> >>
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 01 Apr 2009 09:48:00 +0200
> From: Balazs JOJART <jojartb at pharm.u-szeged.hu>
> Subject: Re: ADL: How to mutate the protein
> To: autodock at scripps.edu
> Message-ID: <49D31C30.70904 at pharm.u-szeged.hu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
> No, it isn't the part of adt, you can download it form the website:
> http://www.ks.uiuc.edu/Research/vmd/
> and see the plugin page as well:
> http://ftp.ks.uiuc.edu/Research/vmd/plugins/
> hope this helps
> Balazs
>
> ishwar chandra wrote:
> > Thanks but please tell VMD is an option in ADT & can we do it using GUI
> of
> > the ADT .
> > Please tell the options  / Procedure.
> > Thanks again
> > On Wed, Apr 1, 2009 at 12:36 PM, Balazs JOJART <
> jojartb at pharm.u-szeged.hu>wrote:
> >
> >
> >> Hello Ishwar,
> >> In vmd you can do the mutation.
> >> Hope this helps,
> >> Balazs
> >>
> >>
> >> ishwar chandra wrote:
> >>
> >>
> >>> Hello Autodockers greetings
> >>> is there any option for  mutating the protein in Autodock . If some one
> >>> knows please reply.
> >>> Thank You.
> >>> Ishwar
> >>> ________________________________________________
> >>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>>
> >>>
> >>>
> >>>
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> >>
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 1 Apr 2009 08:34:25 -0400
> From: Jack Shultz <jshultz at hydrogenathome.org>
> Subject: Re: ADL: [gmx-users] Prepping Docking Complexes
> To: autodock at scripps.edu, nextgame at hotmail.com
> Message-ID:
>        <6c65435e0904010534n7bedfb01qdb2ac7fd897dfb7f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Rob,
>
> I've never used Modeller. Do you suggest I just go through these
> tutorials and get an idea for how to predict the protein structures?
> http://salilab.org/modeller/tutorial/
>
> Jack
>
> On Tue, Mar 31, 2009 at 10:26 PM, rob yang <nextgame at hotmail.com> wrote:
> >
> > The homology model package Modeller is also a very nice alternative.
> >
> >> Date: Tue, 31 Mar 2009 19:45:45 -0500
> >> From: sdarnell at oncology.wisc.edu
> >> To: autodock at scripps.edu
> >> Subject: Re: ADL: [gmx-users] Prepping Docking Complexes
> >>
> >> Just so everyone has the link:
> >>
> >> http://spdbv.vital-it.ch/script_guide.html
> >>
> >> Remember to start your scripts with "please do" and end with "thank
> >> you"... literally.
> >>
> >> ~Steve
> >>
> >>
> >> Jack Shultz wrote:
> >> > I think I found the information on scripting for deepview. Thanks
> >> >
> >> > On Tue, Mar 31, 2009 at 7:17 PM, Jack Shultz <
> jshultz at hydrogenathome.org> wrote:
> >> >
> >> >> Free beer? Do you have any? :-)
> >> >> Its been a while since I've used that app. Can this be done through a
> >> >> command-line script or does it have to be done through the GUI?
> >> >>
> >> >> Jack
> >> >>
> >> >> On Tue, Mar 31, 2009 at 4:29 PM, Steve Darnell
> >> >> <sdarnell at oncology.wisc.edu> wrote:
> >> >>
> >> >>> SwissPDBViewer (a.k.a. DeepView). ?It's not GPL, but it is free (as
> in
> >> >>> beer).
> >> >>>
> >> >>> ~Steve
> >> >>>
> >> >>> --
> >> >>> Steve Darnell
> >> >>> University of Wisconsin-Madison
> >> >>> Madison, WI USA
> >> >>>
> >> >>>
> >> >>> Jack Shultz wrote:
> >> >>>
> >> >>>> I got a cleaner result when I used the grep and cut commands
> described
> >> >>>> in this faq
> >> >>>>
> >> >>>>
> http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock/?searchterm=write
> >> >>>>
> >> >>>> However, certain atoms are missing from residues. Are there any GPL
> >> >>>> tools that will automatically fill in missing atoms for a given
> >> >>>> residue?
> >> >>>>
> >> >>>> Jack
> >> >>>>
> >> >>>> On Tue, Mar 31, 2009 at 9:50 AM, rob yang <nextgame at hotmail.com>
> wrote:
> >> >>>>
> >> >>>>
> >> >>>>> take them out manually.
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>> Date: Mon, 30 Mar 2009 14:33:29 -0400
> >> >>>>>> From: jshultz at hydrogenathome.org
> >> >>>>>> To: autodock at scripps.edu
> >> >>>>>> Subject: Re: ADL: [gmx-users] Prepping Docking Complexes
> >> >>>>>>
> >> >>>>>> I am trying to prep a docking complex for gromacs using pdb2gmx.
> It
> >> >>>>>> does not like the chain terminations "TER"
> >> >>>>>> I prepared these using
> >> >>>>>> write_all_complexes -d out.dlg -r pdb1uwq.pdbqt -o out
> >> >>>>>>
> >> >>>>>> Any way to avoid these breaks in the chain and make it more
> amenable to
> >> >>>>>> GROMACS?
> >> >>>>>>
> >> >>>>>> On Mon, Mar 30, 2009 at 1:20 PM, Justin A. Lemkul <
> jalemkul at vt.edu>
> >> >>>>>> wrote:
> >> >>>>>>
> >> >>>>>>
> >> >>>>>>> Jack Shultz wrote:
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>> Hi Guys,
> >> >>>>>>>>
> >> >>>>>>>> Thanks for previous help. Especially Justin. I got the amber03
> and
> >> >>>>>>>> tip3 water models working through my BOINC project now. But if
> I want
> >> >>>>>>>> to simulate a docking complex, I'm running to some errors
> preparing
> >> >>>>>>>> it. I have not done extensive research on this yet, but I'm
> wondering
> >> >>>>>>>> how I can prep these ligand-receptor complexes so they are
> acceptable
> >> >>>>>>>> to pdb2gmx. Maybe someone can point me in the right direction?
> >> >>>>>>>>
> >> >>>>>>>> -------------------------------------------------------
> >> >>>>>>>> Program pdb2gmx_d, VERSION 4.0.3
> >> >>>>>>>> Source code file: pdb2gmx.c, line: 893
> >> >>>>>>>>
> >> >>>>>>>> Fatal error:
> >> >>>>>>>> Chain identifier 'B' was used in two non-sequential blocks
> (residue
> >> >>>>>>>> 975, atom 7970)
> >> >>>>>>>> -------------------------------------------------------
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>> That means you've split apart chain B. ?If you look at your
> structure
> >> >>>>>>> file,
> >> >>>>>>> you'll find:
> >> >>>>>>>
> >> >>>>>>> ATOM ? 7934 ?NE2 HIS B 489 ? ? 126.270 ?67.930 ?67.564 ?1.00
> 47.43
> >> >>>>>>> ?-0.221
> >> >>>>>>> NA
> >> >>>>>>> ATOM ? 7935 ?OXT HIS B 489 ? ? 132.243 ?66.924 ?65.753 ?1.00
> 43.53
> >> >>>>>>> ?-0.646
> >> >>>>>>> OA
> >> >>>>>>> HETATM 7937 ?C ? ACT B1490 ? ? 116.586 ?88.801 ?86.875 ?1.00
> 67.39
> >> >>>>>>> 0.186
> >> >>>>>>> C
> >> >>>>>>> HETATM 7938 ?O ? ACT B1490 ? ? 115.409 ?88.588 ?86.537 ?1.00
> 67.73
> >> >>>>>>> ?-0.647
> >> >>>>>>> OA
> >> >>>>>>> HETATM 7939 ?OXT ACT B1490 ? ? 117.292 ?89.696 ?86.359 ?1.00
> 67.35
> >> >>>>>>> ?-0.647
> >> >>>>>>> OA
> >> >>>>>>> HETATM 7940 ?CH3 ACT B1490 ? ? 117.160 ?87.930 ?87.956 ?1.00
> 67.32
> >> >>>>>>> 0.109
> >> >>>>>>> C
> >> >>>>>>> TER ? ?7941 ? ? ?ACT B1490
> >> >>>>>>> ATOM ? ? ?1 ?O1 ?0.0 d 000 ? ? 125.675 ?63.107 ?72.217 ?0.00
> ?0.00
> >> >>>>>>> ?-0.348
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? ?2 ?C1 ?0.0 d 000 ? ? 125.252 ?63.738 ?73.407 ?0.00
> ?0.00
> >> >>>>>>> 0.292
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? ?3 ?O3 ?0.0 d 000 ? ? 124.554 ?64.931 ?73.121 ?0.00
> ?0.00
> >> >>>>>>> ?-0.348
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? ?4 ?C4 ?0.0 d 000 ? ? 124.318 ?65.780 ?74.249 ?0.00
> ?0.00
> >> >>>>>>> 0.179
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? ?5 ?C6 ?0.0 d 000 ? ? 123.970 ?64.972 ?75.543 ?0.00
> ?0.00
> >> >>>>>>> 0.180
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? ?6 ?C7 ?0.0 d 000 ? ? 123.396 ?63.571 ?75.233 ?0.00
> ?0.00
> >> >>>>>>> 0.183
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? ?7 ?C8 ?0.0 d 000 ? ? 124.363 ?62.784 ?74.308 ?0.00
> ?0.00
> >> >>>>>>> 0.204
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? ?8 ?C5 ?0.0 d 000 ? ? 125.509 ?66.741 ?74.382 ?0.00
> ?0.00
> >> >>>>>>> 0.198
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? ?9 ?O4 ?0.0 d 000 ? ? 126.073 ?66.914 ?73.114 ?0.00
> ?0.00
> >> >>>>>>> ?-0.398
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 10 ?H8 ?0.0 d 000 ? ? 125.582 ?66.394 ?72.473 ?0.00
> ?0.00
> >> >>>>>>> 0.209
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 11 ?O5 ?0.0 d 000 ? ? 125.109 ?64.795 ?76.367 ?0.00
> ?0.00
> >> >>>>>>> ?-0.390
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 12 ?H9 ?0.0 d 000 ? ? 124.827 ?64.626 ?77.270 ?0.00
> ?0.00
> >> >>>>>>> 0.210
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 13 ?O7 ?0.0 d 000 ? ? 122.126 ?63.780 ?74.623 ?0.00
> ?0.00
> >> >>>>>>> ?-0.390
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 14 ?H14 0.0 d 000 ? ? 122.027 ?63.183 ?73.878 ?0.00
> ?0.00
> >> >>>>>>> 0.210
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 15 ?O6 ?0.0 d 000 ? ? 123.684 ?61.791 ?73.545 ?0.00
> ?0.00
> >> >>>>>>> ?-0.388
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 16 ?H13 0.0 d 000 ? ? 124.232 ?61.529 ?72.802 ?0.00
> ?0.00
> >> >>>>>>> 0.210
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 17 ?C2 ?0.0 d 000 ? ? 125.085 ?63.646 ?71.046 ?0.00
> ?0.00
> >> >>>>>>> 0.187
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? 18 ?C3 ?0.0 d 000 ? ? 123.849 ?62.820 ?70.568 ?0.00
> ?0.00
> >> >>>>>>> 0.183
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? 19 ?C12 0.0 d 000 ? ? 123.639 ?62.990 ?69.062 ?0.00
> ?0.00
> >> >>>>>>> 0.204
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? 20 ?C11 0.0 d 000 ? ? 124.937 ?62.624 ?68.251 ?0.00
> ?0.00
> >> >>>>>>> 0.288
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? 21 ?O10 0.0 d 000 ? ? 126.135 ?62.786 ?69.012 ?0.00
> ?0.00
> >> >>>>>>> ?-0.349
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 22 ?C10 0.0 d 000 ? ? 126.147 ?63.869 ?69.925 ?0.00
> ?0.00
> >> >>>>>>> 0.180
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? 23 ?O2 ?0.0 d 000 ? ? 124.007 ?61.412 ?70.818 ?0.00
> ?0.00
> >> >>>>>>> ?-0.390
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 24 ?H4 ?0.0 d 000 ? ? 124.394 ?60.991 ?70.048 ?0.00
> ?0.00
> >> >>>>>>> 0.210
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 25 ?O11 0.0 d 000 ? ? 123.229 ?64.326 ?68.826 ?0.00
> ?0.00
> >> >>>>>>> ?-0.388
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 26 ?H22 0.0 d 000 ? ? 123.738 ?64.694 ?68.100 ?0.00
> ?0.00
> >> >>>>>>> 0.210
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 27 ?O9 ?0.0 d 000 ? ? 125.021 ?63.316 ?67.003 ?0.00
> ?0.00
> >> >>>>>>> ?-0.369
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 28 ?H19 0.0 d 000 ? ? 125.159 ?62.682 ?66.295 ?0.00
> ?0.00
> >> >>>>>>> 0.212
> >> >>>>>>> HD
> >> >>>>>>> ATOM ? ? 29 ?C9 ?0.0 d 000 ? ? 127.585 ?64.061 ?70.409 ?0.00
> ?0.00
> >> >>>>>>> 0.198
> >> >>>>>>> C
> >> >>>>>>> ATOM ? ? 30 ?O8 ?0.0 d 000 ? ? 128.253 ?62.824 ?70.315 ?0.00
> ?0.00
> >> >>>>>>> ?-0.398
> >> >>>>>>> OA
> >> >>>>>>> ATOM ? ? 31 ?H15 0.0 d 000 ? ? 127.660 ?62.167 ?69.944 ?0.00
> ?0.00
> >> >>>>>>> 0.209
> >> >>>>>>> HD
> >> >>>>>>> OA^M
> >> >>>>>>> ATOM ? 7873 ?CB ?PRO B 482 ? ? 123.510 ?77.736 ?70.316 ?1.00
> 27.76
> >> >>>>>>> 0.034
> >> >>>>>>> C ^M
> >> >>>>>>> ATOM ? 7874 ?CG ?PRO B 482 ? ? 124.070 ?78.915 ?71.107 ?1.00
> 27.76
> >> >>>>>>> 0.027
> >> >>>>>>> C ^M
> >> >>>>>>>
> >> >>>>>>> Chains need to be continuous, so don't insert molecules within
> other
> >> >>>>>>> molecules!
> >> >>>>>>>
> >> >>>>>>> -Justin
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>> Workunit information
> >> >>>>>>>> http://hydrogenathome.org/result.php?resultid=1412984
> >> >>>>>>>>
> >> >>>>>>>> Original complex
> >> >>>>>>>>
> >> >>>>>>>>
> http://hydrogenathome.org/sample_results/2559_1uwq_1238414317.pdb.tar.gz
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>> --
> >> >>>>>>> ========================================
> >> >>>>>>>
> >> >>>>>>> Justin A. Lemkul
> >> >>>>>>> Graduate Research Assistant
> >> >>>>>>> ICTAS Doctoral Scholar
> >> >>>>>>> Department of Biochemistry
> >> >>>>>>> Virginia Tech
> >> >>>>>>> Blacksburg, VA
> >> >>>>>>> jalemkul[at]vt.edu | (540) 231-9080
> >> >>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> >>>>>>>
> >> >>>>>>> ========================================
> >> >>>>>>> _______________________________________________
> >> >>>>>>> gmx-users mailing list ? ?gmx-users at gromacs.org
> >> >>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> >>>>>>> Please search the archive at http://www.gromacs.org/searchbefore
> >> >>>>>>> posting!
> >> >>>>>>> Please don't post (un)subscribe requests to the list. Use the
> www
> >> >>>>>>> interface
> >> >>>>>>> or send it to gmx-users-request at gromacs.org.
> >> >>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>> --
> >> >>>>>> Jack
> >> >>>>>>
> >> >>>>>> http://www.facebook.com/home.php#/profile.php?id=832713248
> >> >>>>>> http://hydrogenathome.org
> >> >>>>>>
> >> >>>>>> ________________________________________________
> >> >>>>>> --- ADL: AutoDock List ?---
> http://autodock.scripps.edu/mailing_list ---
> >> >>>>>>
> >> >>>>>>
> >> >>>>> _________________________________________________________________
> >> >>>>> Experience all of the new features, and Reconnect with your life.
> >> >>>>> http://go.microsoft.com/?linkid=9650730
> >> >>>>> ________________________________________________
> >> >>>>> --- ADL: AutoDock List ?---
> http://autodock.scripps.edu/mailing_list ---
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>> ________________________________________________
> >> >>> --- ADL: AutoDock List ?---
> http://autodock.scripps.edu/mailing_list ---
> >> >>>
> >> >>>
> >> >>
> >> >> --
> >> >> Jack
> >> >>
> >> >> http://www.facebook.com/home.php#/profile.php?id=832713248
> >> >> http://hydrogenathome.org
> >> >>
> >> >>
> >> >
> >> >
> >> >
> >> >
> >> ________________________________________________
> >> --- ADL: AutoDock List ?--- http://autodock.scripps.edu/mailing_list---
> >
> > _________________________________________________________________
> > Share photos with friends on Windows Live Messenger
> > http://go.microsoft.com/?linkid=9650734
> > ________________________________________________
> > --- ADL: AutoDock List ?--- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Jack
>
> http://www.facebook.com/home.php#/profile.php?id=832713248
> http://hydrogenathome.org
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 1 Apr 2009 19:08:57 +0530 (IST)
> From: raghu bhagavat <rag_vocal at yahoo.co.in>
> Subject: ADL: Grid co-ordinates!!!
> To: autodock at scripps.edu
> Message-ID: <964429.59484.qm at web94712.mail.in2.yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
> Hello all........
> I have a query in AD Vina version........
> the configuration file has to be given with x, y, z coordinates for
> building the grid...What if we dont know where the ligand has to
> bind.....This will arise in while doing Virtual screening......
> When we use Autodock4 version on command line, the "auto" option is done if
> the grid-centre is not specified and it runs taking the option
> "auto"..........But unlikely in Vina version..........
>
> So for mass operations (Virt. Screening), how to proceed for this problem??
>
> Kindly suggest
>
>
>
>      Add more friends to your messenger and enjoy! Go to
> http://messenger.yahoo.com/invite/
>
> ------------------------------
>
> Message: 6
> Date: Wed, 1 Apr 2009 11:33:42 -0400
> From: "Haipeng hU" <hhu2 at emory.edu>
> Subject: ADL: Autodock problem for Grid generation
> To: "autodock" <autodock at scripps.edu>
> Message-ID: <200904011133417811360 at emory.edu>
> Content-Type: text/plain;       charset="gb2312"
>
> Hi,
>
>     I just begin to use autodock to do some molecular docking. I met a
> problem in the grid generation step. In the tutorial, you should 'set map
> types' based on a ligand when preparing the GPF file. Is that means I should
> generate a grid file for each of my ligand, since I have a bounch of ligands
> need to be docked into the same binding site of a macromolecule. If not,
> some of my ligand contain CL or F atoms, so there is no CL.map or F.map that
> can be used in the docking step. Can anybody help me solve this problem?
> Thanks
>
> Haipeng Hu
>
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 56, Issue 1
> ***************************************
>


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