If you have not already done so, you might try looking here: https://pdb2pqr.readthedocs.io/en/latest/using/examples.html#parameterizing-ligands-with-the-pdb2pqr-web-server. You need to apply the right partial charges to your small molecule with PSB2PQR to be able to apply APBS to it.
The version of PyMOL that you installed with apt-get is probably the open source version. Next time, please include your operating system. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Physiology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center, Rm. 466 975 NE 10th Street<https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466 Oklahoma City, OK 73104-5419 Central Time Zone (follows Daylight Savings Time) office: (405) 271-8300 lab: (405) 271-8313 Faculty webpage<https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> Director: Laboratory of Biomolecular Structure and Function (X-ray crystallography lab)<https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function> Ex-chair: SSRL Users Executive Committee<https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members> Charter member: NIH Maximizing Investigators’ Research Award B (MRAB) Study section<https://public.csr.nih.gov/StudySections/DBIB/MBBC/MRAB> Guest-editor: Special Issue "Nucleic Acid Crystallography Volume II"<https://www.mdpi.com/journal/crystals/special_issues/Nucleic_Acid_Crystallography> submission deadline June 25, 2024 Co-Chair: Oklahoma Data Science Workshop<https://mediasite.ouhsc.edu/Mediasite/Channel/python> ________________________________ From: Luigi Marongiu, PhD <marongiu.lu...@proton.me> Sent: Sunday, November 26, 2023 8:17 AM To: Luigi Marongiu, PhD <marongiu.lu...@proton.me> Cc: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>; pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol 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. Sent with Proton Mail<https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!91FP9SLBNsqS8eThZ_0UNDUVLqeM5sdLcs0RhpVWuFCYTgv9UkS6FbV83OX2HQXD-I2v7ruXzzTA7TXsjauNBxLT5p2XpyGj$> secure email. On Sunday, November 26th, 2023 at 1:13 PM, Luigi Marongiu, PhD via PyMOL-users <pymol-users@lists.sourceforge.net> wrote: Hello, I am using Version 2.5.0, if I not mistaken, I installed it via apt-get: sudo apt-get -y install pymol In the legacy tab, there is nothing... Thank you On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu> wrote: Hi Luigi , Please include the version of PyMOL that you are using. The APBS Tools are under the "legacy plugins" in the incentive version (2.5.7). These are absent in the open source PyMOL (2.5.0). There was a relatively recent change in the Python libraries used to generate the widgets in PyMOL. You may have gotten an error about a missing Pnw module when trying to load the plugin with a recent version of the open source PyMOL. To use the plugin on the Wiki, you try an older version of PyMOL. Hopefully, someone who is more knowledgeable about plugins will provide a better answer. Best regards, Blaine ________________________________ From: Luigi Marongiu, PhD via PyMOL-users <pymol-users@lists.sourceforge.net> Sent: Saturday, November 25, 2023 2:02 AM To: pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net> Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol Hello, I tried to install APBS by launching Plugin manager and giving the URL of the app: http://www.pymolwiki.org/index.php/apbsplugin<https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$> 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.
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