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Questions related to Atoms
In a QM/MM job, I got this error Include all MM classes Angle bend undefined between atoms 5983 5985 6621 OW-HW-HW [H,H,L] Angle bend undefined between atoms 5985 6621 6619...
24 March 2022 8,952 2 View
Dears, If there any open source (program) to plot the Nanopartciles and attach ligands. From such structure I would like to calculate the DFT? kind regards
24 March 2022 3,518 5 View
I am looking at a problem related to the Clausius-Mossotti equation. The Clausius-Mossotti equation is given by, chi = (4*pi*n*alpha)/ (1 - 4*pi*n*alpha/3) where, chi: susceptibility n: number...
22 March 2022 9,035 3 View
Hello everyone, My lammps input script is as following : units real variable cfac equal 1.01325e-4 variable cunits string GPa atom_style full boundary p p p pair_style lj/cut/coul/cut...
21 March 2022 3,217 2 View
I have a site disordered system, with multiple ions at particular site. I need to refine the occupancies maintaining the chemical formula and total occupany of 100% in fullprof. I tried giving...
19 March 2022 3,731 7 View
I am trying to perform a docking between my enzyme and the substrate using AutoDock Vina but the output of the program is a strucutre with atoms bond even when they are far, unnatural torsions......
16 March 2022 8,326 3 View
When i performed MD simulation with step: gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro (define box 1.1 x 1.1 x 0.8),the results exhibited as: Generating solvent...
14 March 2022 615 4 View
Hello, I have been trying to obtain a single point using DLPNO-CCSD(T) but in some cases, I have obtained the following error: "ORCA finished by error termination in MDCI Calling Command: mpirun...
10 March 2022 6,595 1 View
Im looking for a multi sequence structural alignment tool that can align main chain atoms like main chain oxygen and main chain nitrogens in a PDB file. Or even better, one that specifically...
07 March 2022 7,449 2 View
Hello, I am modelling a polycrystalline CoCrNi medium-entropy alloy, into which I am trying to dope Aluminium atoms using MD simulations. I am trying to replace some of the CoCrNi atoms in the...
06 March 2022 7,121 3 View
Hello all Actually, I want to perform text classification using Bert algorithm on a text dataset that is imbalanced . I want to balance my data but first convert text to vector and then balance my...
04 March 2022 4,234 3 View
I have trouble understanding how to generate these files, because a pseudo potential is not necessary for the electron, and do I need to specify the electron in the POSCAR?
03 March 2022 2,733 2 View
I am running a DFT-D3 geometry optimization with ORCA5.0 of a condensed system (a portion of a pdb file; no metal ions). What I did? - I assumed it to be a closed-shell system but applied UKS...
03 March 2022 6,996 3 View
I need to assembly gold nanoparticles with calixarene. How dithiol molecules enter the cavity of cuproaromatics and bond with gold atoms.
27 February 2022 6,046 1 View
One of the most valuable properties that allows the 1H-NMR spectrum to give structural information is spin-spin coupling, which is caused by spin coupling between hydrogen nuclei that are not...
26 February 2022 6,390 4 View
I have a protein simulated. I want to measure the angle between two domains (domain II & IV) and use the third domain (domain III) as a hinge between them. First, I want to select center of...
25 February 2022 2,861 3 View
Hello all, I’m an undergraduate working on structure calculation for a protein – ligand complex for months but haven’t got any satisfying results so far. The following is my protocol and criteria...
24 February 2022 2,245 0 View
Hi All, I am using QE to do bader analysis. I Have generated the necessary files by using "http://theory.cm.utexas.edu/henkelman/code/bader/". But my question is this code gives bader charge file...
24 February 2022 8,059 0 View
What is a PSO algorithm (in optimization)? What are some examples of its applications? Thanks!
24 February 2022 5,201 3 View
I am sure that I am getting an underestimated bandgap in nanotube. But it is not feasible to do a Hybrid Functional calculation for such a large complex structure. How would anyone suggest me to...
22 February 2022 3,510 1 View
Could someone help me, I have a cif file and I want to perform electronic structure calculations in abinit or qe, however, when viewing the cif file, it presents several identical structures...
22 February 2022 1,590 3 View
Hello, I am trying to fit the atom. I tried to match PEG to density, because my crystallization condition contains PEG. But I can see the appearance of negative density after refinement. What...
22 February 2022 1,307 3 View
Hello, Can anyone recommend a tool for measuring the orientation angle between two domains of a protein? Thanks
22 February 2022 4,474 3 View
Dear all, Im looking for a tool that would help me find the binding sites of a given set of TFs, I have tried Ciider but wasn't able to get it working on my machine.
21 February 2022 183 3 View