Tag: SCF

Dear all, I am facing an issue while running AIMD simulations of a box of ~1000 atoms. The system is an amorphous MOF made of Fe linked by benzene tricarboxylate (named Fe-BTC). I use PBE functional with DZVP basis set and GTH pseudopotential ; DIIS method and…

Dear all, I have been trying to optimize a unit cell of the 2D semiconductor CrSBr using GPW method implemented in CP2K. The initial cell parameters were a = 3.6 A, b = 4.8 A and c = 25.0 A (obtained from previous calculations with Quantum Espresso and in good…

Annotation of short-read scRNA-seq data with isoform-level information Using fluorescence-activated cell sorting (FACS), we isolated the Lineage-negative, cKit (Cd117) positive (LK) cell fraction of mouse bone marrow cells, a population containing stem and progenitor cells14 from young (8 weeks old, n = 3) and aged (72+ weeks old, n = 3) mice. We generated…

Newswise — A gene regulating the F-Box and WD Repeat Domain Containing 7 (FBXW7) protein is frequently mutated or deleted in various types of human cancer, including gynecological cancers. Such FBXW7 mutations have been associated with poor prognosis due to increased resistance to treatment. Hence, detection of the FBXW7 mutation…

Cells and cell culture KOPN30, BV173, and K562 are BCR/ABL1-positive leukemia cell lines. All leukemia cell lines, as well as Ba/F3 cells, were maintained in RPMI-1640 medium supplemented with 15% fetal bovine serum (FBS) and penicillin–streptomycin (100 U/mL) at 37 °C in an atmosphere containing 5% CO2. KOPN30 cells were obtained…

Dear CP2K users and developers: I am investigating the oxygen transport path in perovskite with CI-NEB. In order to consider DFT+U and generate “.model” file, I have to give up K-point and build a big cell with 250 atoms. I set 9 REPLICA. My computer doesn’t have enough memory(My computer…

Hello everyone,   Can anybody please help me with the following error in my error file? I have recently installed cp2k 8.2 version using intel-minimal.psmp arch file with intel 2018 compiler, gcc and fftw. Please guide me with job script and compilation.     forrtl: severe (174): SIGSEGV, segmentation fault…

Hi everyone, I have a single node server with two Xeon Gold 6154 CPU @ 3.00GHz, 18 cores each, 36 total, 72 threads. I have tested several NPROC_REP values in a series of vibrational analysis runs started with the following command:mpirun -np 72 –bind-to hwthread  cp2k.psmp -i cp2k.inp -o cp2k.out…

Hello everyone, I have a simple (100) copper slab (100 atoms, 4 layer==> see input.xyz); and I am trying to make the overall charge of my system equal to +1.39. Since the CHARGE tag only takes integers, I am trying to give partial charges to the atoms in the top…

Review . 2023 Mar 14;13:1147239. doi: 10.3389/fonc.2023.1147239. eCollection 2023. Affiliations Expand Affiliations 1 Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China. 2 Qingdao Cancer Institute, Qingdao, China. 3 School of Basic Medicine, Qingdao University, Qingdao, China. 4 Department of Pharmacology, School of Pharmacy, Qingdao University,…

FBXW7 is a member of the F-box protein family, which functions as the substrate recognition component of the SCF E3 ubiquitin ligase. FBXW7 is a main tumor suppressor due to its ability to control proteasome-mediated degradation of several oncoproteins such as c-Jun, c-Myc, Cyclin E1, mTOR, and Notch1-IC. FBXW7 inactivation…

Introduction Diabetic nephropathy (DN) is a type of severe complication of diabetes mellitus (DM) and is the main cause of chronic kidney disease (1). Various of mechanism are reported to be involved in the pathogenesis and development of DN, such as hyperglycemia, oxidative stress (2), mitochondrial dysfunction (3), endoplasmic reticulum…

Overview Product name Description Rabbit polyclonal to Fbxw7 Host species Rabbit Tested applications Species reactivity Reacts with: Mouse, Rat, Human Immunogen Recombinant full length protein…

Hi Janson   I would say that nothing «unexplainable” happened, just read the CP2k output. CP2K informs you that the “SCCS iteration cycle did not converge in 200 steps”. This happened already in the first SCF iteration step and thus everything thereafter becomes unreliable. The reasons for convergence failure can…

Dear cp2k developers and users, Recently I am trying to calculate pdos of a slab system and I am curious about if it is possible to obtain with ROKS instead of UKS scheme. However when I switched to ROKS, scf procedure ends normally but pdos calculation terminates with error segmentation…

Hello everyone, I have a list of differential genes (list1) and another list where I have the ID of the genes and the name (list2) and I want to name the genes from list1 taking the name from list2, how can I do this? I will appreciate your support, thanks….

Description Monoclonal Anti-FBXW7 antibody produced in mouse has been used in Western blotting and immunohistochemistry. F-box proteins are associated with various signaling pathways, such as nutrient sensing in yeast, conserved developmental pathways in plants and animals. These proteins mediate recognition of phosphorylated targets including Cyclin E, Myc, c-Jun, and Notch,…

Here is how you can get the structure from PubChem, read the SMILES into Avogadro2, do a MMFF94 (classical) optimization, and then a single-point energy calculation using NWChem (RHF, 6-31G*). The Avogadro2 Input builder will create a CP2K file if you prefer. For GROMACS, there is extensive documentation that includes…

Dear CP2K users, I’m struggling with convergence for bulk Fe, i.e. 3x3x3 supercell containing 54 Fe atoms. I wanted to simulate adsorption of different organic molecules on Fe(100) slab later, so this is my starting point. During GEO_OPT or CELL_OPT runs I sporadically encounter SCF issues like this: …    33 Broy./Diag….

Introduction Klebsiella pneumoniae (Kp; K. pneumoniae) is an important hospital and community-acquired pathogen that primarily causes pneumonia, urinary tract infections, bloodstream-associated infections, meningitis, and pyogenic liver abscess.1–3 Carbapenem antibiotics represent the most important treatment for Enterobacteriaceae; however, with the widespread use of such antibiotics, carbapenem-resistant K. pneumoniae (CRKP) is increasingly…

Hello, I am trying to sort a GFF file using the FASTA index output from samtools faidx. Both of my input files have content, but when I use the command below to sort my GFF, I get no output to the screen or file. bedtools sort -faidx F._oxysporum_f._sp._cubense_UK0001.fna.fai -i ../Mimps/F._oxysporum_f._sp._cubense_UK0001.fna_mimp_hits.gff…

The National Institute of Pharmaceutical Education & Research (NIPER), SAS Nagar is an autonomous Institute of National importance set up by the Government of India, Ministry of Chemicals & Fertilizers by an Act of Parliament, to impart higher education and undertake advanced research in the field of Pharmaceutical sciences, technology…

Introduction This tutorial is designed to illustrate how to relax the structureof a system (without changing the cell dimensions) using CP2K. Weuse the relaxation of a water (H\(_2\)O) molecule as an example. The example files are contained in geometry_optimisation.tgz that comes with this tutorial. The calculation was carried out with…

Organisation of the Pregap4 Manual Introduction Summary of the Files used and the Processing Steps Introduction to the Pregap4 User Interface Introduction to the Files to Process Window Introduction to the Configure Modules Window Introduction to the Textual Output Window Introduction to Running Pregap4 Pregap4 Menus Pregap4 File menu Pregap4…

The Staden Package Mini-Manual – Viewing Traces Using Trev For some types of sequencing project it is convenient to view and edit the chromatogram data prior to assembly into a gap4 database, and this is the function of the program trev. Trev displays the original trace data, its base calls…

F-box and WD repeat domain containing 7 (FBXW7) acts as a substrate receptor of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase and plays crucial roles in the regulation of several cellular processes, including cell growth, division, and differentiation, by targeting diverse key regulators for degradation. However, its role in regulating cellular senescence…

Using a permanently unlocked form of the plant enzyme MAX3, UC Davis researchers are exploring the mechanism by which the plant hormone strigoractone regulates a massive network of genes controlling plant growth and architecture. Credit: Nitzan Shabek/UC Davis As sessile organisms, plants have to continually adapt their growth and architecture…

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

Dear CP2K users, I am performing geometry optimizations for Pt slab (fcc111) with one hydroxyl (OH) radical on top. First, the cell optimization of bulk Pt (fcc111) is performed and successfully converged (Pt_cellopt.xyz).  However, when I put one OH radical on Pt 111 to perform geometry optimization, I observed a…

Altman, B. J., Stine, Z. E. & Dang, C. V. From Krebs to clinic: glutamine metabolism to cancer therapy. Nat. Rev. Cancer 16, 619–634 (2016). CAS  Article  Google Scholar  Hensley, C. T., Wasti, A. T. & DeBerardinis, R. J. Glutamine and cancer: cell biology, physiology, and clinical opportunities. J. Clin….

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

Hello All, I created a Ti2CO2 monolayer (MXene)  that I will attach as an xyz file. I want to run GEO_OPT on this structure with periodic boundary conditions only in the XY directions. In my output RESULTS file  the first SCF converges in 106 steps, but then the file is…

Dear cp2k users and experts, I want to use ASE as a job submission tool on supercomputer and further I plan to use ASE to perform Genetic Algorithm global optimization. However, I find for relatively large system containing more than 200 atoms (generated by GA, so it is always a…