From owner-chemistry@ccl.net Tue Nov 3 08:46:00 2020 From: "Andrea Mauri andrea.mauri|a|alvascience.com" To: CCL Subject: CCL: alvaDesc 2.0 - molecular descriptors and fingerprints Message-Id: <-54205-201103084242-1824-IUvi+NwhUtjJ9X94q3glPw###server.ccl.net> X-Original-From: "Andrea Mauri" Date: Tue, 3 Nov 2020 08:42:40 -0500 Sent to CCL by: "Andrea Mauri" [andrea.mauri%%alvascience.com] Dear all, We are happy to inform you that we have just released the version 2.0.0 of alvaDesc. Here is the list of the main changes: - the descriptors can be explored using a spreadsheet-like table with sorting and filtering capabilities - PCA data can be exported to tab-separated text files - in addition to PCA, the t-SNE algorithm can be used for dimensionality reduction - the 'Lasso selection' can be used to select molecules in all charts many 3D descriptors (e.g., 3D Atom Pairs) can be calculated on molecule having 3D coordinates only on the molecular skeleton (i.e., having no 3D coordinates for H atoms) - if needed, the partial charges are calculated using the Gasteigers "Partial Equalization of Orbital Electronegativity" (PEOE) More than 300 descriptors have been added, for the full list check the website and here are some: - Constitutional descriptors: number of aromatic atoms (nAA), number of sp3 hybridized carbons/total carbon count (Fsp3) - Ring descriptors: number of spiro atoms (nSpiro),number of bridgehead atoms (nBridgeHead),aromatic proportion (AP) - Information indices: Bertz complexity index (BertzCT) - 2D matrix-based descriptors on Laplace matrix: algebraic connectivity (also known as Fiedler value or Fiedler eigenvalue) - P_VSA-like descriptors on partial charges - ETA indices: eta composite index for reference alkane (Eta_R) and eta local composite index for reference alkane (Eta_LR) - 3D matrix-based descriptors on Coulomb matrix - Atom-type E-state indices: E-state minimum and E-state maximum - Molecular properties: Wildmann-Crippen molar refractivity (MR99) and consensus molar refractivity, Wildmann-Crippen octanol-water partition coefficient (LOGP99) and consensus LogP, ESOL: Estimated SOLubility (logS) for aqueous solubility, SAscore: Synthetic Accessibility score (SAscore), Plane of best fit (PBF) - Drug-like indices: Quantitative Estimation of Drug-likeness (QED) - WHALES descriptors https://doi.org/10.1038/s42004-018-0059-2 - MDE descriptors https://doi.org/10.1021/ci970109z - Chirality descriptors https://doi.org/10.1002/cmdc.201700798 New versions of alvaModel and alvaRunner have been released to be fully compatible with alvaDesc v2.0.0. Best regards, Andrea Mauri Andrea Mauri, PhD mail - andrea.mauri{=}alvascience.com Alvascience srl - http://www.alvascience.com/ From owner-chemistry@ccl.net Tue Nov 3 09:20:01 2020 From: "Tobias Kraemer Tobias.Kraemer|mu.ie" To: CCL Subject: CCL:G: [EXTERNAL] CCL:G: Gaussian error in Frequency Calculation Message-Id: <-54206-201103085853-7464-+XnL05Gx6p2S1Kvs9KdyKg++server.ccl.net> X-Original-From: Tobias Kraemer Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 3 Nov 2020 13:58:43 +0000 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [Tobias.Kraemer(-)mu.ie] Hi all, Thanks for all your suggestions regarding this issue that I reported yesterday. There seem to be a number of possible causes (D3 corrections, memory...), and many of you have suggested some potential solutions to the problem. We will explore these and hopefully this can be resolved. It is a rather puzzling problem, but it is good to know that some others have experienced the same. As I mentioned, in all my years of using Gaussian I cannot recall ever seeing this behaviour. Thanks again for your input on this issue, and I am glad that this wasn't such an obscure problem after all. Best, Tobias Dr. Tobias Krämer Lecturer/Assistant Professor Department of Chemistry and Hamilton Institute Maynooth University, Maynooth, Co. Kildare, Ireland. E: tobias.kraemer^mu.ie   T: +353 (0)1 474 7517 -----Original Message----- > From: owner-chemistry+tobias.kraemer==mu.ie^ccl.net On Behalf Of Tobias Kraemer tobias.kraemer .. mu.ie Sent: 02 November 2020 21:11 To: Tobias Kraemer Subject: [EXTERNAL] CCL:G: Gaussian error in Frequency Calculation *Warning* This email originated from outside of Maynooth University's Mail System. Do not reply, click links or open attachments unless you recognise the sender and know the content is safe. Sent to CCL by: "Tobias Kraemer" [tobias.kraemer[-]mu.ie] Hello all, I hope everyone is well. I haven't posted here for a long time, but I have encountered some strange behaviour in a Gaussian frequency calculation that I have not seen before. There seems to be little to no information out there on this problem, so I was hoping to get some input from the list. Essentially, we are running a geometry optimisation with subsequent frequency job (same input) at the B3LYP/6-311+G(d) level of theory and including the GD3BJ dispersion correction. The molecule is a small molecules containing potassium. The optimisation furnishes a perfectly fine structure, but the calculation then error terminates with the following message Maximum of*** iterations exceeded in RedStp. All entries in this section contain NaN entries, e.g. Frequencies -- NaN NaN NaN Red. masses -- NaN NaN NaN Frc consts -- NaN NaN NaN IR Inten -- NaN NaN NaN Atom AN X Y Z X Y Z X Y Z 1 19 NaN NaN NaN NaN NaN NaN NaN NaN NaN 2 6 NaN NaN NaN NaN NaN NaN NaN NaN NaN 3 1 NaN NaN NaN NaN NaN NaN NaN NaN NaN 4 1 NaN NaN NaN NaN NaN NaN NaN NaN NaN 5 6 NaN NaN NaN NaN NaN NaN NaN NaN NaN 6 6 NaN NaN NaN NaN NaN NaN NaN NaN NaN Obviously something has gone awfully wrong in the frequencies. The problem can be reproduced by running the frequency job on the optimised geometry alone (here we used a smaller basis set). Interestingly the calculation finishes normally in this case, but shows only NaN entries everywhere in the output. I have seen some indication that this may be related to the D3 correction, but I would like to hear your opinion on this. We are running G09 E.01. your help would be much appreciated. thanks in advance. Kind regards, Tobiashttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 3 17:03:00 2020 From: "=?UTF-8?Q?Bj=c3=b6rn_Sommer?= bjoern++cellmicrocosmos.org" To: CCL Subject: CCL: MolVA 2021 (EuroVis Workshop) - Call for Journal and Conference Papers Message-Id: <-54207-201103160727-3398-ZbFjKskF3MIb5GxKtfxoPg(-)server.ccl.net> X-Original-From: =?UTF-8?Q?Bj=c3=b6rn_Sommer?= Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 3 Nov 2020 22:07:18 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Bj=c3=b6rn_Sommer?= [bjoern(_)cellmicrocosmos.org] Dear Colleagues, (apologies for cross-posting) We are happy to announce an open call for submissions to the Computers and Graphics Journal (C&G) Special Section on Molecular Graphics and Visual Analysis of Molecular Data. We invite original research, system, and survey papers that summarize and expand the state of the art in visualization and computer graphics with a strong focus on applications to molecular data. Important Dates ************************************************************************ Submission portal open: 1.10.2020 Submission deadline: 31.1.2021 First decision notification: one month after the submission (latest on 28.2.2021) Final decision notification: three months after the submission (latest on 30.4.2021) ************************************************************************ We solicit several types of submissions: Journal paper submissions presenting original work within the scope described below. Survey papers discussing the state-of-the-art topics relevant to MolVA Workshop (tinyurl.com/molva). Extended and revised versions of full papers, short papers, and surveys that were accepted only for presentation at the MolVA 2021. All submissions will be fully peer-reviewed by at least three experts according to the standards of Computers and Graphics Journal. You can find the complete author guidelines at: https://www.elsevier.com/journals/computers-and-graphics/0097-8493/guide-for-authors. The papers might be accepted either as journal publications or conference-only publications. The journal publications will be published directly in Computers and Graphics journal, while the conference-only papers will be published in EG Digital Library. The conference-only publications will be offered to submit an extended version that will undergo another fully peer-reviewed process and could be still accepted as a journal publication after the workshop. After the first round of reviews the authors will be notified about the track that was selected for their paper based on the quality of the publication and may choose to retract the paper if they do not wish to accept it. Please submit your contribution via Editorial Manager (Deadline: February 28, 2021): https://www.editorialmanager.com/CAG/default.aspx All accepted papers will be presented at MolVA 2021 Workshop, which will be co-located with EuroVis 2021 in Zurich, Switzerland. Therefore, at least one of the authors of an accepted paper will have to register and attend the workshop. Suggested topics for papers include, but are not limited to: - Molecular Graphics & Rendering - Web-based Molecular Graphics & Visualization - Immersive Analytics approaches using, e.g., VR/AR technologies - Visual Analysis of Molecular Data (e.g., molecular structures, biological networks and pathways, or omics data) - Visualization of Dynamic Molecular Data & Large Molecular Systems - Machine-learning approaches for analysis of molecular data - Tools papers describing new molecular visualization tools or novel features in existing tools Best regards,    Jan ByÅ¡ka, Michael Krone, Björn Sommer    CaG Guest Editors    MolVA 2021 Organizing Committee