Cpptraj: RMSD as a function of Residue Number?

I have the AMBER 10ns MD trajectory, I want to calculate the average RMSD over all snapshots for each residue. Would you please tell me where I can get the cpptraj script to plot RMSD vs Residue...

10 November 2016 4,533 3 View

Gnuplot: simultaneously multiply and divide $1 in gnuplot.

Hi! Can someone tell me how I can simultaneously multiply and divide $1 in gnuplot, like I have divided $1 previously using following script without rewrite data file. splot 'dssp.gnu' using...

10 November 2016 1,353 3 View

Multiply whole column with a value (Shell Programming and Scripting)?

07 August 2016 4,716 2 View

Query regarding MD Simulation of a protein with an elongated active site?

Dear all,I am interested to run MD simulation to look closer into the mode of interactions between different ligands and protein. My target protein is a homotetramer and I have selected it's chain...

06 July 2016 9,530 12 View

Does anyone know, how to make active site conserve water unique before loading pdb on xleap?

I want to run MD, but my problem is conserve water of my target protein active site. Six conserve water molecules are present in active site. When I load complex pdb on xleap, then after adding...

31 December 2015 724 1 View

Troubles in understanding, amber minimization input?

Dear all, I am a beginner at amber and I have some troubles in understanding, amber minimization input file flags. I am using the following script for minimzation, Minimization Amber12 &cnrl...

31 December 2015 1,806 2 View

Any advice on the atom type error after resp charge calculation using gaussian?

I want to optimize reference ligand of my target protein (1M48) before running Molecular Dynamic Simultion. I have prepared reference ligand mol2 file through moe and then convert it into com...

11 December 2015 7,127 3 View

Is the aminoacid sequence of PDE-1 type 5 venom of Bothrops atrox available?

I am unable to find amino acids sequence of PDE-1 type 5 venom of bothrops atrox in any sequence database. I am interested to target this protein for computational studies. Kindly guide me, if...

31 December 2014 2,003 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

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

Difficulties purifying Outer Membrane Vesicles using a Sucrose Density Gradient: Unable to detect any protein after this process?

I'm currently trying to purify Outer Membrane Vesicles (OMVs) following their extraction from the bacteria I'm working with. After the initial extraction the concentration of protein seems good...

27 January 2021 6,852 3 View