ADL: free pdb file creation

Garrett M. Morris garrett at
Thu Mar 6 17:13:20 PST 2008

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< 
> >
> *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:
> 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'.


> I hope this would be helpful for you
> Best,
> Tomek Wlodarski
> On Thu, Mar 6, 2008 at 12:17 AM, Larry Layne <llayne at>  
> wrote:
>> Hairat,
>> I've found that The Dundee PRODRG Server (
>> 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> Subject: ADL: pdb files To: <autodock at 
>>> >
>>> 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
>>> _________________________________________________________________  
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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
La Jolla,  CA 92037-1000,  USA.

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