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Questions related to Molecular Dynamics Simulation
I was using fragbuilder module in python to generate peptides of sizes 4, 6, and 10. However, the issue with fragbuilder module is that some of the bond angles are deviating from the standard...
23 May 2023 3,665 4 View
I have lots of pdb files of short peptides of size 18. I tried with dssp. But the issue with dssp in mdtraj module is that it misses the beta strand compeltely as a single strand does not have...
21 May 2023 5,738 0 View
Hello everyone, I am trying to determine relative expression values for specific genes in different life-stages of my organisms (adult, larval, and microfilaria). For each of the three...
11 May 2023 5,215 3 View
During spectroscopic analysis of paclitaxal order from sigma, I am getting the maximum absorption of paclitaxal dissolved in methanol at 211 nm. However, according to the previously reported...
09 May 2023 6,304 2 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 6,172 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 9,609 0 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 3,901 3 View
Can an MD simulation be performed by adding other salts by varying their concentration inside the box?
02 May 2023 9,198 3 View
I have attached the output file. Please help me.
01 May 2023 3,044 9 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 1,390 4 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 8,571 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 6,536 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 6,705 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 9,683 0 View
i want to draw a structure of Mn/NiCo-LDH in Material Studio any body can help me please?
19 April 2023 3,293 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 1,819 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 8,661 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 7,670 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 8,598 1 View
As I am new to the castep I don't know which parameter should be selected for CuO nanoparticle. I want to use LDA+U potentials. I Want the calculations
16 April 2023 2,362 4 View
Hi, dear friends online. I am a fresh person in bioinformatics with little understanding. but I need to learn to analyze RNA-sequencing data. I think python is simple, I want to use it to...
06 April 2023 2,592 3 View
I'm using LUVs as membrane models to study drug-membrane interaction. My composition of liposome is POPC : CHOL. I was confused about the selection of a buffer system for my liposomes. So far, I...
06 April 2023 6,776 3 View
I have already used hydrogen bond plug-in but the graph is showing no hydrogen bonds in all frames.
05 April 2023 8,922 3 View
I'm trying to optimize a large number of structures( above thousand) with 60 atoms in each. I need a cheap method for optimization. I came across DFTB , which can be helpful for my calculation....
02 April 2023 113 3 View