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Questions related to Molecular Dynamics Simulation
Hello every body , I want to know how can i insert my coordinate of orbitals en tight binding model at Pythb formate. thanks in advance
09 May 2023 8,314 0 View
I am trying to determine some mechanical properties of Hf-Nb-Ta-Zr high entropy alloy. But I'm not being able to relax it properly & it's causing absurd values of elastic moduli,...
08 May 2023 6,236 1 View
Hi all, I am trying to use the BFEE plugin in VMD to calculate the free energy of a protein-ligand complex. However, I keep getting the error below when I try to generate the input...
08 May 2023 9,685 0 View
My first Edited book titled "Indian Tourism: Diaspora Perspective" by Emerald Publishing has been indexed in Scopus. While I'm happy, I'm intrigued to know on what basis, the books are selected...
04 May 2023 8,615 3 View
The box size determined for my protein before starting the MD simulation is as in image 1. After 200 ns, some of the protein comes out of the box (image 2). Does this affect the simulation...
03 May 2023 3,989 3 View
After running of python script downloaded from MacKerell lab website a file is generated: ligand_ini.pdb. After viewing it in VMD it does not look like the ligand any more.There is no error in...
03 May 2023 3,193 2 View
Can an MD simulation be performed by adding other salts by varying their concentration inside the box?
02 May 2023 9,272 3 View
I have attached the output file. Please help me.
01 May 2023 3,148 9 View
Hello, I'm interested in surface reaction mechanism. So I read some papers about this. There are two types of papers. 1.DFT calculation(VASP) using NEB method 2.Chemkin mechanism calculation I...
01 May 2023 4,120 0 View
I'm a windows 11 user and I am having problems launching autodock tools 1.5.6 and 1.5.7. The GUI will just launch up to 6-8% and then it will crash and will not continue opening. I already tried...
28 April 2023 1,466 4 View
Hi is there any way to extract intra-molecular distance distribution in a cluster of geometrically optimized cluster of molecules in Gaussian?
27 April 2023 875 2 View
reduction of nitro to amine in ambient conditions using ethanol, methanol, THF etc
26 April 2023 114 4 View
My protein of interest is fused with MBP tag, and it does not contain tryptophan but MBP does. After factor Xa digestion, my protein was separated from MBP, and I eluted my protein while MBP is...
25 April 2023 1,209 2 View
why ligand is getting detached from protein at the complex.gro step when I am generating the ligand toplogy from ATB , swissparam, acpype serverserver? while this problem did not occur while using...
24 April 2023 8,645 1 View
I am performing an all-atom molecular dynamic simulation in LAMMPS to perform the diffusion and adsorption capacities of gaseous hydrogen in metal alloys. For the simulation, I am using an...
24 April 2023 6,604 4 View
After refining the protein structure multiple times, it still fails to pass VERIFY3D. The ERRAT score is 96.9298 and PROCHECK results are fine. What can be done to improve the VERIFY3D results?
24 April 2023 6,810 3 View
I'm working on a virtual screen of approximately 8000 compounds, and I need to select only those that interact specifically with an active site residue. However, it is clearly impossible to...
24 April 2023 9,760 0 View
I have done a mechanistic study (I am a beginner and passionate about computational chemistry) to find the reaction pathway in Jaguar Schrodinger. It is a bulky palladium complex and reactants...
24 April 2023 8,515 5 View
I am facing this error in gromacs, can anyone help me to solve this error.
21 April 2023 3,478 3 View
i want to draw a structure of Mn/NiCo-LDH in Material Studio any body can help me please?
19 April 2023 3,384 1 View
Hi, as my question already indicates I would like to do some multivariate analysis of my proteomics data as I have multiple characteristics in my samples. I have successfully used MetaboAnalyst...
19 April 2023 1,895 3 View
I am conducting a molecular docking study using peptides as ligands. I successfully ran the docking process using autodock vina, and when I viewed it using Discovery Studio, I realized that the...
18 April 2023 8,722 7 View
I am currently trying to develop an assay to test the binding affinity (Kd) of a binding inhibitor to its target, through the displacement of a fluorescent ligand that is pre-bound to the target....
18 April 2023 7,753 1 View
The gold nanoparticle was synthesised through Turkevich method. And also kindly suggest ways to work towards lowering the PDI index.
16 April 2023 8,677 1 View