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Questions related to Atoms
Hello, After doing 100 ns MD simulations to a peptide, I want to determine the trajectory between the side chains of some residue pairs. For example: RSFFSFLGEAGFDG - I want to plot distance vs...
09 March 2021 9,084 3 View
The error statement that I am getting is "module has no method named ‘MolDraw2DCairo’" which I have installed and uninstalled and reinstalled again just to be sure. Any other alternative Python...
06 March 2021 8,723 1 View
during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...
23 February 2021 637 5 View
MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...
22 February 2021 9,759 3 View
Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?
21 February 2021 3,359 5 View
I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...
20 February 2021 1,475 1 View
We want to ONIOM calculation in gaussian16. However, gaussian doesn't work. What should we do? Atom 15 layer R linked to atom 85 is also bonded to atom 161 in layer M bad...
16 February 2021 8,234 3 View
I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...
09 February 2021 7,567 3 View
Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...
07 February 2021 3,042 2 View
I am trying to use the following command in GROMACS to generate a CHARMM topology file: gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top The atom list in my pdb file (amp.pdb)...
02 February 2021 7,933 6 View
When doping in case of semiconductor is concerned, we doped Si by trivalent or pentavalent impurity atoms to improve its electronic properties but in case of nano-particles, sometimes we doped...
01 February 2021 7,325 1 View
I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...
01 February 2021 7,255 3 View
In GROMACS how do I know how many box images a particular atom has moved from from t=0 to t=N? LAMMPS, for example, has the option to include image flags in the dump file for x, y, and z. Is there...
31 January 2021 9,016 3 View
I would like to generate multiple large samples of amorphous silica in LAMMPS. Currently I am generating it by beginning with a lattice of silicon and oxygen atoms and using a melting and...
29 January 2021 6,285 4 View
I have done molecular replacement to build a protein structure however even after a lot of refinement and protein chain fixing the difference between rfree and rwork is around 7%. While solving...
28 January 2021 5,899 6 View
I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...
27 January 2021 4,543 3 View
Dear collegues, as stated - I'm looging for a soft that would calculate electron density on a given atom of a small molecules. Either for Ubuntu 18.04 or latest MacOS. I tried multiwfn, but it...
27 January 2021 4,217 3 View
Hi, I'm doing molecular dynamics on a 168 atoms system with a 20 A vacuum. To speed up my calculations, I set ALGO = Fast tag in INCAR, but surprisingly VASP crashes momentarily!. I have done a...
26 January 2021 10,137 3 View
I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein...
25 January 2021 7,458 3 View
Hi, I have been trying to calculate the frequency vibrations of the excited state S1 of an organic molecule (24 atoms). The geometry optimisation of the excited state converged smoothly howerver...
23 January 2021 1,607 3 View
Hi all, I am trying to perform some ab inito DFT calculations using cp2k code. I have a unit cell of 120 atoms and would like to know how to refine or reduce the number of atoms in the unit cell...
21 January 2021 6,217 3 View
In a trial, I am trying to calculate NICS (0 and 1) values for benzene ring using gaussian09. I have placed the ghost atoms at the center, 1A, and 2A above the rings. On using the method/basis...
20 January 2021 3,352 3 View
I'm a new Vesta learner, I have downloaded cif of Ch3Nh3PbI3. Total number of atom in chemical formula for Ch3Nh3PbI3 is 12. But when i convert this cif to poscar file using Vesta, total number of...
15 January 2021 6,117 11 View
When studying EXAFS and XPS, I often see that "X-rays bounce electrons from atoms". Where will the electrons that are blown off the atoms by X-rays eventually go? In the case of EXAFS, I think...
12 January 2021 1,766 3 View