Importance of RMSD in GROMACS
I want to make schiff base from amino acid and aldehyde but I am not getting any precipitation. I tried using methanol and ethanol as solvent and adding KOH to dissolve the amino acid in the...
19 December 2023 9,627 8 View
What is the best way for High performance liquid chromatography of chlorophyll? What will be the best solvent concentration?
05 October 2023 9,864 2 View
Is 10 mg/mL a reasonable stock solution to start with for 0.1-0.5 mg/mL concentrations?
29 July 2023 7,249 5 View
for example, the needed dose is 400ug/mL, how will I turn my crude extract into 400 ug/mL? p.s my research is about a-glucosidase activity
12 June 2023 9,445 3 View
I have been trying to amplify NEB 5-alpha F'Iq Competent E. coli for my phage display library and therefore need a high transformation efficiency. The commercial product has a TE of 10^9, but I...
06 January 2023 6,360 4 View
I have done a 50 nano second protein simulation using Gromacs and obtained an RMSD value greater than 3 nm. is it ok to proceed with it or is the value incorrect?
26 November 2022 4,865 2 View
I have ran a simulation of a protein structure using Gromos force field and obtained the radius of gyration. Is it mandatory to get a linear plot? How does high or low RoG matters? What it implies...
26 November 2022 8,091 2 View
What is the use of energy range in the config file in autodock vina? What is the normal values?
15 January 2022 7,338 1 View
Hi. I am working with ligands containing Se and Te. It is possible to dock them using AutoDock 4.2 since i have added thwir parameters. But can i do the same with vina? Can we add additional atom...
30 December 2021 8,087 2 View
Hi. Is it mandatory to optimise our ligand before docking using Autodock or Autodock vina? I have not received the structure from any database therefore the structure was drawn using Marvin draw...
29 December 2021 5,619 3 View
In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?
11 July 2024 4,831 0 View
Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...
08 July 2024 4,724 4 View
I have performed a 100 ns md simulation for protein ligand complex .The result generated is found that the complex RMSD is higher than the Apo form.What could be reason for this ? Could anyone...
24 June 2024 9,049 3 View
I have run MD simulation of a protein-protein docked complex for 50ns. The RMSD plot obtained from the simulation is attached here. The RMSD plot shows a stable trajectory for entire simulation,...
09 June 2024 7,886 1 View
Good day! Please tell me, is it correct to compare two structures obtained using homology modelling on the SwissModel website and then compare them using RMSD in PyMOL?
18 May 2024 3,566 1 View
Dear GROMACS expert, I am currently having trouble to analyse the results from my simulations. After processing the output files using this command, gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o...
02 May 2024 6,690 7 View
Hi, I've noticed a common practice in publications where multiple Molecular Dynamics (MD) simulations are conducted with varying initial velocities. However, I'm uncertain about the appropriate...
18 April 2024 6,293 2 View
Aside from defining the disulfide bond, what other reasons could account for the significant difference in RMSD of the docked structure and co-crystal?
15 April 2024 7,706 2 View
I want to calculate the RMSD for the individual confrmations from the output file pdbqt into to run in into a program that only accepts PDB files. I can convert pdbqt files to PDB using openbabel...
25 March 2024 3,075 5 View
Hello. How can I plot in RMSD H-Bond and radious gyrus in VMD in Windows? I ran MD in Namd and y I have all the files Step5.
23 March 2024 7,689 1 View
