I want to targeted MD simulation of macromolecule using AMBER software .As i am quite new to MD simulation field and of such a big complex .
Thank you.I will try using that
After COVID-19 it has seen that EFL learners technological affiliation has raised. In addition, in the post-COVID period learners started to engage AI technologies like ChatGPT while learning...
08 August 2024 8,964 4 View
How we can cite the papers from ResearchGate. I am trying to create citations for this article, Quantum Machine Learning Algorithms for Optimization Problems: Theory, Implementation, and...
08 August 2024 6,690 3 View
I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.
07 August 2024 6,622 1 View
I want to refine one XRD peak of my in-situ xrd but the background is never working good which ultimately fails the refinement. How to refine and adjust the background using GSAS-II
05 August 2024 5,291 2 View
Hi, i would like to simulate an absorption process in Aspen Plus. I want to use the NRTL model und would like to add some individual Henry coefficients. Is that possible and how?
05 August 2024 2,333 2 View
Hello everyone, I'm encountering an issue with my electrochemical impedance spectroscopy (EIS) measurements and would appreciate some insights. Experimental Setup: Electrodes: Gold interdigitated...
05 August 2024 3,783 2 View
AI tools like ChatGPT can enhance research work significantly when used responsibly and in conjunction with thorough human oversight.
05 August 2024 1,842 3 View
Have you ever seen a LC-MS/MS method uses both internal standards and external standards (in matrix matching purpose) but the concentrations of internal standards are outside the calibration curve...
05 August 2024 3,084 6 View
Hi everyone, I am working on brain slices for visualizing a protein in the soma and dendrites, using a fluorescence tag. However, I need a tool (not paid) for reconstruction of the whole neuron,...
04 August 2024 4,725 2 View
Citi BLOC Standard Basket Definitions: A standardized unit representing a fixed basket of construction materials, labor, and equipment costs priced in various cities. Purpose: To create a common...
04 August 2024 8,997 1 View
Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...
06 August 2024 807 3 View
I am working on natural remedies for de-worming in small ruminant livestocks. Part of my project involves formulation of drench-type product, which I have not much experience in. My experience is...
30 July 2024 9,806 1 View
Hello, I am searching for the binding position of a drug in a ribosome, based on previous work indicating it binds there. The resolution of the ribosome-drug Cryo-EM map is around 2.5 Å. I've been...
19 July 2024 2,155 0 View
Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...
17 July 2024 3,472 3 View
I have been able to assign the CHARMM forcefield to my ligand i.e. acetyl coenzyme A but not the amber forcefield. I want to run amber forcefield and the parameterization of ligand is failing. I...
15 July 2024 7,323 1 View
Dear Sir, I hope this message finds you well and in good health. I am writing to seek your guidance regarding an issue I encountered during the annotation of my phage sequence using DNA Master....
30 June 2024 8,650 0 View
Hello, I am doing ONIOM QM/MM energy calculation. I am adding explicit solvent. My input keywords is below: # oniom(m06/6-31g(d,p):amber=hardfirst) scrf=(iefpcm,read,oniompcm=x) nosymm...
04 June 2024 5,825 1 View
Hi, I'm new to QM/MM calculations, and I've recently started a calculation for a laccase enzyme containing 4 Cu ions. Following the Ambertools MCPB.py tutorial, I've created these files:...
30 May 2024 7,237 0 View
Good morning, I am running some Steered molecular dynamics in Amber 22 and want to set some restraints in the z-axis so as to imply certain distances from my ligand to its substrate. My goal is...
27 May 2024 7,082 1 View
Hi all-- I'm preparing plant root samples for RNAseq and have been investigating some samples that had suspicious bands in their lanes when I ran a 1% non-denaturing RNA QC gel. To spot check...
26 May 2024 7,139 1 View