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Questions related to Molecular Dynamics Simulation
Hi, I am looking to conduct rheometric experiments on water or hydrogels whose viscosity is very less. Should I use Dynamic light scattering or a rheometer?
27 June 2023 8,740 14 View
Hello all, I want to run a Molecular dynamics simulation by using Gromacs and OPLS AA force field. I'm getting the above error when I tried to run the energy minimization step. Now I don't...
21 June 2023 1,254 3 View
I have been reading the following article on peptide structure prediction. https://www.biorxiv.org/content/10.1101/2022.02.17.480937v1.abstract I wanted to know whether alpha fold 2 can be used to...
20 June 2023 7,166 6 View
I am trying to visualize the change in the molecular geometry along the reaction path using the output from the Polyrate17-C package for a gas phase addition reaction. As mentioned in the Polyrate...
20 June 2023 5,301 0 View
In this strucutre each Bi atom is coordinated with four oxygen and each each oxygen is cordinated with 2 Bi atom. I find it difficult to understand how this layer is named as (Bi2O2). The charge...
18 June 2023 9,101 0 View
Hi all, I am trying to coordinate zinc to the NMR structure PDB ID: 1sp1 (a C2H2 zinc-finger) using HADDOCK. To make it clear, the PDB structure is zinc coordinated, and I am using it as a system...
15 June 2023 3,795 1 View
PDB Code of protein or name
15 June 2023 1,288 4 View
I performed protein ligand complex simulation in gromacs. To obtain PCA and FEL graph, used gmx covar, gmx anaeig and gmx sham module of gromacs. For further analysis, I am in need of lowest...
13 June 2023 1,283 0 View
I am a M.Sc. student. I have successfully expressed my protein in soluble part using a solubilizing tag. I faced problems in Ni-NTA purification, as protein was not binding to the column. So, I...
13 June 2023 2,935 4 View
Hi, I am using Malvern's Zetasizer to get the rheological properties of the hydrogel formed with Phytagel containing silica beads entrapped in the said hydrogel. When I am taking the readings...
13 June 2023 2,237 7 View
What is the mechanism behind this behavior? Is it due to the longer molecular chain of UHMWPE, which prevents the formation of a crystalline layer?
06 June 2023 9,152 13 View
I ran a molecular dynamics simulation which was interrupted at the penultimate stage due to a power cut.
05 June 2023 5,781 2 View
Hi Collegues, To calculate entropy (T*S) and Gibbs (G) free energy of electroreductions using computational hydrogen electrode (CHE) model (according to this equation, G = E + ZPE - TS + U), can...
05 June 2023 6,650 0 View
I have a protein which has five different components, and these were isolated separately. So is it possible to club these individual fragments together using any tool/software? And if there is/are...
01 June 2023 841 5 View
1. What is the correct pentapeptide sequence of ELPs: GVGVP or VPGVG? 2. Does the sequence "GVGVP" also encode the ELP protein? 3. What differences can be seen if we change the ELP pentapeptide...
01 June 2023 1,003 0 View
I am trying to find out the logic in not identification of hydrogen bond interaction in the charged NH+ from the ligand part with the Asp residue from the protein. That incidence has been observed...
01 June 2023 7,390 0 View
I have the free energy landscape data how do i get this??
28 May 2023 5,222 1 View
I wanted to know whether DSSP assignment hold good for peptide sturctures of size 10 and 18. I have large number of pdb files of peptides of various sequences and of size 6, 10 and 18. Can DSSP...
28 May 2023 5,454 0 View
my work on molecular docking, pharmacokinetics, DFT KINDLY SUGGEST
27 May 2023 3,115 1 View
I need to use the AutoDock program, but I tried both versions 1.5.6 and 1.5.7. I had no problem loading, my only problem is that when I open the program, the loading remains around 9% in the...
23 May 2023 6,193 3 View
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 3,742 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 5,829 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 5,286 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 6,377 2 View