Any Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber?

17 December 2020 1 589 Report

Hi everyone

I'm currently working with a membrane transporter protein to which I need to simulate molecular dynamics (MD). For this, I have inserted my protein in a membrane with CHARMM-GUI and preparing the system with Amber. My problem is that Amber's tutorial to perform MD to this type of proteins only specifically details the process with a membrane without proteins (http://ambermd.org/tutorials/advanced/tutorial16/index.html) and talks very little about what I need to do.

For that reason, will anyone have a tutorial available to do MD for membrane-bound proteins in Amber?

Badges
Science topic

More Andres Ibacache's questions See All

Where can I find atmospheric measurement profiles (temperature, density, etc.) between 300-800 km altitude?

I am investigating thermospheric mass density profiles between 300-800 km altitude. I would like to compare the variability with other parameters, including temperature, electron content,...

01 March 2021 5,902 3 View

How to design a boost converter for a mppt controller?

I have a doubt on how to select the inductor and capacitor value when I want to implement MPPT controller. This is because we always take a maximum output voltage and current but in this case, we...

28 February 2021 3,637 2 View

Jellyfish as food?

We are investigating the acceptance of jellyfish-based food dishes in Latin America. If you are interested in the topic, please fill out the anonymous survey at the following link. Thanks in...

06 December 2020 4,266 2 View

Can anyone explain the calculation process of integrated biomarker response (IBR)? Any specifical software?

Hi. I'm working with soil enzymes and I have an issue because i saw several papers that used "integrated biological response" or IBRv2 to integrate data from enzymes and build a hexagonal star...

11 October 2020 5,131 3 View

Which nutritional component of grains affect the pH level?

Dear community I have a great doubt related to pH in grains. It has been reported that some amino acids could be influencing the pH level. However, could minerals located in the inner parts of...

24 September 2020 6,694 14 View

Is is possible to get the distribution generated graphs on the WEKA GUI Explorer Pre-processing tab?

I'm trying to add the generated distribution graphs to my assay but I cannot find anywhere I can do so. I thought about using the command Line built in, however nothing on the internet nor their...

14 July 2020 2,363 3 View

Main differences between Sulfadimidine and Sulfamerazine?

03 June 2020 3,361 1 View

Beyond individual behavior, are there psychological processes in plants?

Psychological processes as: perception, memory, learning, emotion or motivation?

26 April 2020 7,348 11 View

Can I do a path analysis with AMOS using factor scores as observable variables?

Can I do a path analysis with AMOS using factor scores as observable variables? Can I build a model with latent variables from observable variables derived from factorial scores? Is this...

20 February 2020 7,441 3 View

What is the best approach for E. coli phylogenetics?

I have four whole genomes sequencing of E. coli isolates , and I wanna to classify in phylogenetics groups. Whats is the best ways? Thanks.

24 January 2020 7,302 3 View

what is the simplest definition of ion exchange capacity

What this unit identifies for the ion exchange capacity ca. 0.92 meq. g-1. I am a newcomer in the membrane area. I just started. I highly appreciate your help

08 May 2021 0 0 View

what is the simplest definition of ion exchange capacity

What this unit identifies for the ion exchange capacity ca. 0.92 meq. g-1. I am a newcomer in the membrane area. I just started. I highly appreciate your help

08 May 2021 0 0 View

Dapi fluorescence protocol for colon cell lines ?

28 February 2021 2,534 2 View

Cloudy/high background western blot - can anyone help me?

Hi everyone! I try to detect VDR protein (~48 kDa) using Western Blot. After SDS-PAGE using 10% MP TGX Stain-Free Gel from BioRad I transferred the protein onto an metOH activated PVDF membrane...

23 February 2021 6,266 3 View

Protocol for membrane extraction E. coli?

Hello! I am interested in determining whether a poly-unsaturated fatty acid I have engineered E. coli to produce is being incorporated into the membrane of the cells or if it is simply a free...

21 February 2021 7,447 2 View

How do you prepare a porous crosslinked Polyvinyl alcohol and Glutaraldehyde membrane or film?

I am trying to prepare a Polyvinyl alcohol membrane for carbondioxide adsorption

08 February 2021 7,493 3 View

Background and spots in Western Blot membrane?

Do you know why my membrane looks like this? I did this western for Anti-hnRNP D/AUF1 antibody ab50692, as primary antibody in 1:1000 overnight at 4c and Anti-rabbit IgG HRP linked antibody...

07 February 2021 5,591 4 View

Acoustic simulation of Membrane?

I have 1 mm thick membrane. This membrane is perforated. I want to simulate this in Acoustic module of comsol. For this ,which type of module I can use in comsol.?

02 February 2021 2,505 6 View

Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...

31 January 2021 7,091 3 View

Can i re-incubate a WB membrane with a higher solution of the previously used 1ry ab?

I've incubated my western-blot membrane with both primary and secondary antibodies and i just realized at the end that i've used a lower concentration of my primary antibody for my loading control...

27 January 2021 1,034 3 View