ADL: help needed for evaluating the results

Liu Ji zjuliuji at
Fri Apr 10 17:23:09 PDT 2009


Were you informed with any errors when you opened the receptor file? You
should be sure that your marcomolecule was opened in ADT. In most cases, the
path to file should not contain any special characters. You can open the
molecule from the File-->Read molecule firstly. If it is opened, there will
be a molecule representation in ADT. You can use mouse to perform the
zoom/transition/rotation of the molecule for an ideal view. Then choose it
by Analyze-->Macromolecule-->Choose... for analysis.
BTW, people always use the Display-->show/hide molecule option to show or
hide molecules, or click the square just after the molecule name on the

Good luck
2009/4/10 Husniye Irmak Cataloglu <irmakc at>

>  We applied till 4th exercise but we sticked at it's 2nd step.
> 2. Visualize binding in a pocket by displaying molecular surfaces:
> In the Dashboard, click on the circle under MS in the ind row
> and in the hsg1_rigid row. Click on the diamond under Atom
> to color the ligand surface by the element of the underlying
> atom. Click on the diamond under DS to color hsg1_rigid by
> David Goodsell colors.
> This view of the docking allows you to see how the docked ligand
> 'fits' into the macromolecule. Clicking on the circles under MS allows
> you to show and hide the various msms surfaces.
> We can't see the macremolecule whatever we do. We just can see the ligand.
> Why can it be?
> On Sat 04 Apr 2009 12:41:07 EEST, Liu Ji wrote:
>  Hi Cataloglu,
>> You can always use ADT to do analysis. Seriously did you read through the
>> tutorial? The answers you need are well described in the first four
>> exercises.
>> Liu Ji
>> 2009/4/4 Husniye Irmak Cataloglu <irmakc at>
>>>  Hello all. We made a docking using Autodock 4.0 and applied all the
>>> steps
>>> in the Autodock tutorial. However, we have some problems in the
>>> evaluation
>>> part.
>>> Where can we see the free energy and how can we see the ligand and
>>> protein
>>> in the active binding site? Thanks everyone for your help.
>>> Irmak Çataloğlu
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