ADL: autodock Digest, Vol 87, Issue 17

Samanthi Handunnetti De Silva sthabr1 at tigers.lsu.edu
Sun Nov 20 18:09:13 PST 2011


Thanks for the support. I was able to carry out calculations without a
problem earlier. I have changed two things in my new calculations;

1. Instead of 1RTJ now I'm using a new pdb file 2YKN as the macromolecule(
I came to notice that this new protein is missing one important amino acid
residue in the binding pocket.)

2. Instead of MM2 energy minimized chemdraw structures, I'm using saved
Gaussian output files as pdb files.

The protein 2YKN has very good resolution and crystallographic structure
but it's missing PHE227 which is an important amino acid residue in the
binding pocket. I know there's a way to add missing residues but I need to
know whether making such changes would have an adverse effect on final
calculations.

I cannot use Gaussian output files directly for the calculation; therefore
I have to save the output file as a pdb. Please help me on this regards.

Thanks,

Samanthi


On Sun, Nov 20, 2011 at 2:00 PM, <autodock-request at scripps.edu> wrote:

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> Today's Topics:
>
>   1. Re:  autodock Digest, Vol 87, Issue 16 (Lenin Dom?nguez)
>   2. Re:  How to know flexible residues in flexible docking
>      (Lenin Dom?nguez)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 19 Nov 2011 12:30:52 -0800
> From: Lenin Dom?nguez <acheron24 at hotmail.com>
> Subject: Re: ADL: autodock Digest, Vol 87, Issue 16
> To: "autodock at scripps.edu" <autodock at scripps.edu>
> Message-ID: <BLU0-SMTP4036CFE6017AE024E54C9EDB5C50 at phx.gbl>
> Content-Type: text/plain; charset="utf-8"
>
> For the PDB coming out from NAMD, try to parse it through VMD or UCSF
> Chimera. Maybe those would help you get a "standard" PDB.
>
> I don't remember all the details of how different NAMD residue
> nomenclature is but you could probably manually change HISE, HISD or HISP
> residue back to regular HIS.
>
> Do you have Dropbox? That way you could share your files without sending
> attachments to the list.
>
> Quienes odian a los gatos, volver?n como ratones en la pr?xima vida.
>
> -Faith Resnick
>
>
> On Nov 19, 2011, at 12:00, autodock-request at scripps.edu wrote:
>
> > Send autodock mailing list submissions to
> >    autodock at scripps.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >    http://mgldev.scripps.edu/mailman/listinfo/autodock
> > or, via email, send a message with subject or body 'help' to
> >    autodock-request at scripps.edu
> >
> > You can reach the person managing the list at
> >    autodock-owner at scripps.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of autodock digest..."
> >
> >
> > Today's Topics:
> >
> >   1.  Could anyone help me please?? (Normand? Morrison)
> >   2. Re:  Could anyone help me please?? (Mihaly Mezei)
> >   3. Re:  Could anyone help me please?? (Stefano Forli)
> >   4.  Thnx for the advice... (Normand? Morrison)
> >   5.  Thnx for the advice... (Normand? Morrison)
> >   6.  Support (Samanthi Handunnetti De Silva)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 18 Nov 2011 18:53:25 +0000
> > From: Normand? Morrison <normandemorrison at hotmail.com>
> > Subject: ADL: Could anyone help me please??
> > Message-ID: <SNT105-W16210845C4EB5470E05D98C6C40 at phx.gbl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> > I've used autodock to generate some pdbqts before, yet this time, I'm
> using a resulting pdb from a molecular dynamics simulation (NAMD). During
> this simulation, one of the commands is to change HIS to HSE... so I
> thought this could be the error, and though I've changed it back to HIS on
> the pdb, I'm still getting several errors while trying to generate my pdbqt.
> >
> > When I try to add the polar hydrogens, an error message appears telling
> me that it could not find an atomic number for M M.
> > Another series of errors is when I'm trying to choose this pdb as the
> macromolecule, using Grid (autodock tools). It tells me that some charges
> need to be corrected on the written pdb file. If I overlook this and
> proceed to save the macromolecule as a pdbqt file, it tells me: could not
> create the file, all atoms do not have an autodock_element field... This
> error comes even after trying to assing the AD4 element (edit --> atoms -->
> assign AD4 type), as well as merging non-polar hydrogens. When overlooking
> this too, a window appears, indicating that HG1, HE2, HH1, HH2, HD2... etc
> do not have a charge.
> >
> > So, the only difference is that I'm using a pdb generated from a
> molecular dynamics simulation, and yet I don't know what to do to correct
> all these errors...
> >
> >
> > .Normand? Morrison.
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 18 Nov 2011 17:30:38 -0500
> > From: Mihaly Mezei <Mihaly.Mezei at mssm.edu>
> > Subject: Re: ADL: Could anyone help me please??
> > To: autodock at scripps.edu
> > Message-ID: <f66bb4f85de2.4ec6963e at mssm.edu>
> > Content-Type: text/plain; charset=us-ascii
> >
> > Hi,
> >
> > your molecule probably was distroted at a few places, so some bonds
> appear to be broke and that confuses ADT. Try a short minimization of the
> final structure and see it ADT likes it better.
> >
> > Mihaly Mezei
> >
> > Department of Structural and Chemical Biology, Mount Sinai School of
> Medicine
> > Voice:  (212) 659-5475   Fax: (212) 849-2456
> > WWW (MSSM home):
> http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
> > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> > WWW (Department): http://atlas.physbio.mssm.edu
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 18 Nov 2011 14:33:27 -0800
> > From: Stefano Forli <forli at scripps.edu>
> > Subject: Re: ADL: Could anyone help me please??
> > To: "autodock at scripps.edu" <autodock at scripps.edu>
> > Message-ID: <4EC6DD37.7010002 at scripps.edu>
> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> >
> > Hi Normand?,
> >
> > I agree with Mihaly's hypothesis, especially if an MD is involved.
> > Another thing thing that could help you to 'sanitize' a bit the input
> PDB could be to
> > pre-process the file with OpenBabel, with PDB as both input and output
> format. Sometimes
> > this helps to fix atom name misalignments and/or exotic naming
> conventions.
> >
> > Hope this helps,
> >
> > Stefano
> >
> > On 11/18/2011 02:30 PM, Mihaly Mezei wrote:
> >> Hi,
> >>
> >> your molecule probably was distroted at a few places, so some bonds
> appear to be broke and that confuses ADT. Try a short minimization of the
> final structure and see it ADT likes it better.
> >>
> >> Mihaly Mezei
> >>
> >> Department of Structural and Chemical Biology, Mount Sinai School of
> Medicine
> >> Voice:  (212) 659-5475   Fax: (212) 849-2456
> >> WWW (MSSM home):
> http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
> >> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> >> WWW (Department): http://atlas.physbio.mssm.edu
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >
> >
> > --
> >  Stefano Forli, PhD
> >
> >  Research Associate
> >  Olson Molecular Graphics Laboratory
> >  Dept. Molecular Biology,  MB-112
> >  The Scripps Research Institute
> >  10550  North Torrey Pines Road
> >  La Jolla,  CA 92037-1000,  USA.
> >
> >     tel: (858) 784-2055
> >     fax: (858) 784-2860
> >     email: forli at scripps.edu
> >     http://www.scripps.edu/~forli/
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Sat, 19 Nov 2011 17:36:58 +0000
> > From: Normand? Morrison <normandemorrison at hotmail.com>
> > Subject: ADL: Thnx for the advice...
> > To: Autodock <autodock at scripps.edu>
> > Message-ID: <SNT105-W1694E56A438E5BF794E6C2C6C50 at phx.gbl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> > Thanks a lot for the advice... will run a new shoerte MD... it's gotta
> be it...
> >
> >
> > .Normand? Morrison.
> >
> >
> >
> >> Date: Fri, 18 Nov 2011 14:33:27 -0800
> >> From: forli at scripps.edu
> >> To: autodock at scripps.edu
> >> Subject: Re: ADL: Could anyone help me please??
> >>
> >> Hi Normand?,
> >>
> >> I agree with Mihaly's hypothesis, especially if an MD is involved.
> >> Another thing thing that could help you to 'sanitize' a bit the input
> PDB could be to
> >> pre-process the file with OpenBabel, with PDB as both input and output
> format. Sometimes
> >> this helps to fix atom name misalignments and/or exotic naming
> conventions.
> >>
> >> Hope this helps,
> >>
> >> Stefano
> >>
> >> On 11/18/2011 02:30 PM, Mihaly Mezei wrote:
> >>> Hi,
> >>>
> >>> your molecule probably was distroted at a few places, so some bonds
> appear to be broke and that confuses ADT. Try a short minimization of the
> final structure and see it ADT likes it better.
> >>>
> >>> Mihaly Mezei
> >>>
> >>> Department of Structural and Chemical Biology, Mount Sinai School of
> Medicine
> >>> Voice:  (212) 659-5475   Fax: (212) 849-2456
> >>> WWW (MSSM home):
> http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
> >>> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> >>> WWW (Department): http://atlas.physbio.mssm.edu
> >>> ________________________________________________
> >>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> >>
> >> --
> >>  Stefano Forli, PhD
> >>
> >>  Research Associate
> >>  Olson Molecular Graphics Laboratory
> >>  Dept. Molecular Biology,  MB-112
> >>  The Scripps Research Institute
> >>  10550  North Torrey Pines Road
> >>  La Jolla,  CA 92037-1000,  USA.
> >>
> >>     tel: (858) 784-2055
> >>     fax: (858) 784-2860
> >>     email: forli at scripps.edu
> >>     http://www.scripps.edu/~forli/
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Sat, 19 Nov 2011 17:38:20 +0000
> > From: Normand? Morrison <normandemorrison at hotmail.com>
> > Subject: ADL: Thnx for the advice...
> > To: Autodock <autodock at scripps.edu>
> > Message-ID: <SNT105-W6A2F0845D6587B0144ADDC6C50 at phx.gbl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> > Thank you very much for the advice... will run a new shorter MD... this
> one was 50 ns...
> >
> >
> > .Normand? Morrison.
> >
> >
> >
> >> Date: Fri, 18 Nov 2011 17:30:38 -0500
> >> From: Mihaly.Mezei at mssm.edu
> >> To: autodock at scripps.edu
> >> Subject: Re: ADL: Could anyone help me please??
> >>
> >> Hi,
> >>
> >> your molecule probably was distroted at a few places, so some bonds
> appear to be broke and that confuses ADT. Try a short minimization of the
> final structure and see it ADT likes it better.
> >>
> >> Mihaly Mezei
> >>
> >> Department of Structural and Chemical Biology, Mount Sinai School of
> Medicine
> >> Voice:  (212) 659-5475   Fax: (212) 849-2456
> >> WWW (MSSM home):
> http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
> >> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> >> WWW (Department): http://atlas.physbio.mssm.edu
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Sat, 19 Nov 2011 12:53:27 -0600
> > From: Samanthi Handunnetti De Silva <sthabr1 at tigers.lsu.edu>
> > Subject: ADL: Support
> > To: autodock at scripps.edu
> > Message-ID:
> >    <CAFm5OVD869zA+2Red1jp1ipCL_zPcwBni_+F2iBD3GotCzsZ8Q at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi,
> > I got the following erreor message when I tried to run a docking
> > simulation. Please help me.
> > Traceback (most recent call last):
> >  File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\ViewerFramework\VF.py", line 735, in tryto
> >    result = apply( command, args, kw )
> >  File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\AutoDockTools\autoanalyzeCommands.py", line 2848, in
> > doit
> >    d.readDlg(dlgFile)
> >  File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\AutoDockTools\Docking.py", line 83, in readDlg
> >    self.ch = ConformationHandler(self.ligMol,
> > AttributeError: Docking instance has no attribute 'ligMol'
> > Thanks,
> > Samanthi
> >
> >
> > ------------------------------
> >
> > ________________________________________________
> > --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
> >
> > End of autodock Digest, Vol 87, Issue 16
> > ****************************************
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 19 Nov 2011 12:39:44 -0800
> From: Lenin Dom?nguez <acheron24 at hotmail.com>
> Subject: Re: ADL: How to know flexible residues in flexible docking
> To: "autodock at scripps.edu" <autodock at scripps.edu>
> Message-ID: <BLU0-SMTP388760A4AD00B36F5C52BB6B5C50 at phx.gbl>
> Content-Type: text/plain; charset="us-ascii"
>
> I have check the papers recommended for the topic of flexible receptors.
> They do address the question but the implementation is in commercial
> software not AD. However, at least one of then points to a accessible to do
> it:
>
> Check if there homologous or ligand-bound structures of your receptor of
> interest. Then take note of the residues that vary position. Also check B
> factors or different occupancies.
>
> >From there, it is up to you. You could start by making residues with few
> rotamers flexible and evaluate the results.
>
> Let us know what you decide and how it worked for you.
>
>
> On Nov 17, 2011, at 12:00, autodock-request at scripps.edu wrote:
>
> > Re: ADL: How to know flexible residues in flexible docking
>
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 87, Issue 17
> ****************************************
>


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