ADL: free pdb file creation

Rajiv Ranjan Singh rajssai at nii.res.in
Thu Mar 6 07:26:22 PST 2008


hello to all ADL users.
I have some queries regarding autodock.
for preparation of receptor file of a tetrameric protein i downloaded pdb file
and then removed water molecule and ligands thereafter whether i should
minimize the energy of tetrameric protein before preparation of pdbqs file of
the tetrameric protein or not please let me know.

Rajiv
NII, NEW DELHI
INDIA.





On Thu, 6 Mar 2008 10:58:11 +0100, 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.
> 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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--Rajiv Ranjan Singh
Molecular Sciences Laboratory
National Institute of Immunology
Aruna Asaf Ali Marg
New Delhi -110067
INDIA.



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