How old is the version of the RDKit that you are using?
If you are using the most recent version, AllChem.EmbedMolecule() will use
the correct parameters by default.
-greg
On Fri, Jul 6, 2018 at 6:28 PM Phuong Chau <[email protected]> wrote:
> I tried the code: AllChem.EmbedMolecule(x, params = AllChem.ETKDGv2())
>
> but it shows me the error:
> AttributeError: 'module' object has no attribute 'ETKDGv2'
>
> How do I fix this problem? I imported rdkit.Chem and AllChem.
>
>
> On Fri, Jul 6, 2018 at 10:03 AM, Sereina <[email protected]>
> wrote:
>
>> The default conformer generator in RDKit is plain distance geometry,
>> which is known to not be able to provide perfectly flat aromatic rings.
>> You can use the ETKDG conformer generator instead:
>>
>> AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
>>
>> Best,
>> Sereina
>>
>>
>> On 6 Jul 2018, at 17:54, Phuong Chau <[email protected]> wrote:
>>
>> Follow up question regarding to PDB file:
>>
>> Thank you for your help. I was able to create the non-zero coordinates of
>> the chemical. However, when I tried to view it on VMD, the chemical that I
>> used is c1ccccc1 (benzene). The ring itself (and the atoms coming off it,
>> which are mostly hydrogens) should all be in-plane but the pdb file shows
>> that it is slightly puckered. Would anyone explain this for me? How can I
>> make it be in-plane ?
>>
>> Here is a screenshot of the molecule.
>> <Screenshot from 2018-07-06 09-53-12.png>
>>
>>
>> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss <
>> [email protected]> wrote:
>>
>>> On 7/5/2018 1:39 PM, Paolo Tosco wrote:
>>>
>>> As the PDB format includes no stereochemistry, no coordinates are
>>>> needed, and by default they are zero, as the molecule does not have a
>>>> conformation yet.
>>>>
>>>
>>> Hmm. One could argue that PDB format *is* 3D coordinates, so a block
>>> with all zeroes is quite pointless. And of course counter-intuitive.
>>>
>>> Dima
>>>
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Phuong Chau
>> Smith College '20
>> Engineering Major
>>
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>>
>
>
> --
> Phuong Chau
> Smith College '20
> Engineering Major
>
> ------------------------------------------------------------------------------
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