NAMD tuitorial for Membrane Bound Protein Complex Structure.

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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 4,648 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 1,526 3 View

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

Hi, I need to multiply 1st column (comma seperated) of entire file by a value say 2 without disturbing file format. Suppose the file is: 1.000 1.000 0 1.000 2.000 ...

07 August 2016 4,840 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 9,621 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 812 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 1,975 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 7,230 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 2,128 3 View

What is the reason I get 400nm nanoparticles using an extruder with 200 nm membrane for cell membrane coating?

I am trying to coat my micelles and PLGA based nanoparticles with cell membrane using an Avanti mini extruder according to literature . I use 200nm membrane but my particles end up to be 400nm And...

30 July 2024 3,294 3 View

Does it exist some special technique for cutting ceramic membranes for Cross-sectional FESEM images?

Does it exist some special technique for cutting ceramic membranes for Cross-sectional FESEM or SEM images?

25 July 2024 5,482 2 View

Issues with Malaria Coated Nitrocellulose Membrane Releasing Moisture?

Hello, I am currently working with Malaria Pf/Pan nitrocellulose membranes coated for malaria detection. After drying the coated membranes in an Incubator (overnight at 37°C), I've noticed that...

16 July 2024 7,937 1 View

How can we test a Nafion membrane ?

we have a nafion 117 membrane and we want to know if it has the properties claimed by the sellers. what are the tests available ?

13 July 2024 503 1 View

How to wash capsule filters (Membrane: polyethersulfone; pore size0.2u/0.45u) after filtration. can I wash by NaOH? if yes, what will be the molarity?

11 July 2024 8,969 1 View

How can I solve this problem with my western blot?

I have this problem with my western blot for the ABCG2 antibody on nitrocellulose membrane. Help please

02 July 2024 8,715 2 View

How to insert cholesterol inside DPPC membrane by replacing same number of DPPC molecules in GROMACS?

I am trying to insert cholesterol inside the DPPC membrane by using gmx insert_molecules -replace. But number of DPPC molecules replaced is much higher than the number of cholesterol inserted?...

30 June 2024 4,160 2 View

How to assess bacterial permeability?

Is there an established protocol to measure the permeability of bacterial membranes? Thank you

30 June 2024 6,614 3 View

Hello friends In simulating the drug with the liposome, which side of the liposome membrane is the drug placed on? The top leaf or the other?

Several times by placing a restriction on the upper part of the membrane with the aim of preventing the drug from being added from this side, we tried to keep the drug at the top of the leaf, but...

29 June 2024 9,688 1 View

immunofluorescence, False Positive Nuclear Staining in Hydrogel-Embedded Breast Cells?

I have primary breast cells embedded in the hydrogel. When stained with EpCAM without the hydrogel, the staining was correctly localized to the membrane as expected! However, after embedding in...

28 June 2024 353 1 View