ADL: [gmx-users] Prepping Docking Complexes

Jack Shultz jshultz at hydrogenathome.org
Wed Apr 1 05:34:25 PDT 2009


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
>> >>>>>>>
>> >>>>>>> ========================================
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>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>> --
>> >>>>>> Jack
>> >>>>>>
>> >>>>>> http://www.facebook.com/home.php#/profile.php?id=832713248
>> >>>>>> http://hydrogenathome.org
>> >>>>>>
>> >>>>>> ________________________________________________
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>> >>>>>
>> >>>>
>> >>>>
>> >>>>
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>> >>>
>> >>>
>> >>
>> >> --
>> >> Jack
>> >>
>> >> http://www.facebook.com/home.php#/profile.php?id=832713248
>> >> http://hydrogenathome.org
>> >>
>> >>
>> >
>> >
>> >
>> >
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-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org



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