Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol

[Luigi M. P. <mar...@pr...>]

Hello,
I installed PyMol 2.5.7 and ran APBS electrostatic. However, I got the error:

Error encountered: No heavy atoms found. You may also see this message if PDB2PQR does not have parameters for any residue in your protein.

The point is: I am evaluating molecules (acesulfame potassium, in this case) and not whole proteins. If the APBS has worked but could not compute, then I the answer is asnwered.
Thank you.

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On Sunday, November 26th, 2023 at 1:13 PM, Luigi Marongiu, PhD via PyMOL-users <pym...@li...> wrote:

> Hello,
> I am using Version 2.5.0, if I not mistaken, I installed it via apt-get:
>
> sudo
>
> apt-get
>
> -y
>
> install
>
> pymol
>
> In the legacy tab, there is nothing...
> Thank you
>
> On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
>
>> Hi Luigi ,
>>
>> Please include the version of PyMOL that you are using.
>> The APBS Tools are under the "legacy plugins" in the incentive version (2.5.7).
>> These are absent in the open source PyMOL (2.5.0).
>>
>> There was a relatively recent change in the Python libraries used to generate
>> the widgets in PyMOL. You may have gotten an error about a missing Pnw module
>> when trying to load the plugin with a recent version of the open source PyMOL.
>> To use the plugin on the Wiki, you try an older version of PyMOL.
>> Hopefully, someone who is more knowledgeable about plugins will provide a better answer.
>>
>> Best regards,
>>
>> Blaine
>>
>> ---------------------------------------------------------------
>>
>> From: Luigi Marongiu, PhD via PyMOL-users <pym...@li...>
>> Sent: Saturday, November 25, 2023 2:02 AM
>> To: pym...@li... <pym...@li...>
>> Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol
>>
>> Hello,
>> I tried to install APBS by launching Plugin manager and giving the URL of the app:
>>
>> [http://www.pymolwiki.org/index.php/apbsplugin](https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$)
>>
>> The file has been written in ~/.pymol/startup but I got the error:
>>
>> Plugin "apbsplugin" has been installed but initialization failed.
>>
>> How do I properly launch this app? Please note I relaunched PyMol several times.
>> Thank you.
>>
>> Sent with [Proton Mail](https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$) secure email.