ADL: free pdb file creation

Tomek Wlodarski tomek.wlodarski at gmail.com
Sat Mar 8 02:58:14 PST 2008


Hi Garrett!

Thank you for clarify this point!
Best,

Tomek

On Fri, Mar 7, 2008 at 2:13 AM, Garrett M. Morris <garrett at scripps.edu>
wrote:

>
> Hi Everyone,
>
> On 6 Mar, 2008, at 1:58 am, Tomek Wlodarski wrote:
>
> > Hi!
> > PRODRG is a very nice way of doing this but I think it has some
> > disadvantages:
> > - without energy minimization structures are very unreal
> > - with EM are not the best option for AD because in ref: Huey, R.,
> > Morris,
> > G. M., Olson, A. J. and Goodsell, D. S. (2007), A Semiempirical Free
> > Energy
> > Force Field with Charge-Based
> > Desolvation<
> http://www3.interscience.wiley.com/cgi-bin/abstract/114107459/ABSTRACT
> > >
> > *J. Computational Chemistry*, *28*: 1145-1152
> > Authors claim that extended form of ligand is better option for
> > docking than
> > compacted(after EM)
> > I suggest also very easy to use CORINA:
> > http://www.molecular-networks.com/online_demos/corina_demo.html
> > It generates ligand structures in extended form.
>
> Thanks, Tomek, for your valuable pointers to calculating structures of
> the ligand.
>
> I wanted to clarify one point: the comparison of extended, compact and
> same-as-bound ligand conformations was done when modelling the
> _unbound_ form of the ligand, not the _input_ conformation of the
> ligand found in the input ligand PDBQT file.
>
> The scoring function in AutoDock 4 subtracts the internal energy of
> the unbound ligand from that of the docked ligand in order to estimate
> the free energy of binding.  In AutoDock 4.0.1, there are two ways to
> specify the unbound ligand's energy: either by using the "unbound
> <float>" keyword in the DPF, or by using the
> "compute_unbound_extended" keyword.
>
> Note that AutoDock 3 and 4 (currently) derive the bonding in the input
> ligand using distance criteria, so it _is_ a good idea to use a low-
> energy conformation of the ligand without steric clashes for your
> input PDBQT, but it is _not_ a prerequisite that the input ligand's
> conformation be 'extended'.
>
> Garrett
>
> >
> > I hope this would be helpful for you
> > Best,
> >
> > Tomek Wlodarski
> >
> > On Thu, Mar 6, 2008 at 12:17 AM, Larry Layne <llayne at andrew.cmu.edu>
> > wrote:
> >
> >> Hairat,
> >>
> >> I've found that The Dundee PRODRG Server (
> >> http://davapc1.bioch.dundee.ac.uk/programs/prodrg/) has a nice
> >> program
> >> that allows you to create PDB files among other popular types.  By
> >> clicking
> >> on the "draw molecule with JME" link, it will input the structure
> >> into the
> >> text box further down the screen and then give you the choice in
> >> the type of
> >> file format you want it in.  I found it to be very good when I need a
> >> program to  preserve conjugated aromatic carbons.  All they ask for
> >> in
> >> return is to cite them in any publications.
> >>
> >> Happy Docking!
> >> Larry
> >>
> >>> ----------------------------------------------------------------------
> >>>
> >>> Message: 1 Date: Wed, 5 Mar 2008 03:26:23 +0000 From: Hairat Sabit
> >>> <hairat at hotmail.com> Subject: ADL: pdb files To: <autodock at scripps.edu
> >>> >
> >>> Message-ID: <BAY140-W3932DA4E36AFC69350CC1C8110 at phx.gbl> Content-
> >>> Type:
> >>> text/plain; charset="iso-8859-1"
> >>>
> >>>
> >>> Dear all, What are the good softwares (free) to generate small
> >>> molecules
> >>> .pdb or .mol2 files for Autodock?I appreciate your inputs.Hairat
> >>> _________________________________________________________________
> >>> Shed
> >>> those extra pounds with MSN and The Biggest Loser!
> >>> http://biggestloser.msn.com/
> >>>
> >>> ------------------------------
> >>>
> >>
> >> ________________________________________________
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> >>
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>
> ___
> Dr Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)
>
> The Scripps Research Institute,       tel: (858) 784-2292
> Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
> 10550  North Torrey Pines Road,       email: garrett at scripps.edu
> La Jolla,  CA 92037-1000,  USA.       mgl.scripps.edu/people/gmm
>
>
>
>
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