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

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

NAMD tuitorial for Membrane Bound Protein Complex Structure.

03 April 2015 6,859 2 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

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...

03 March 2021 2,870 3 View

What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

I'm dealing with a mediation model and am using the PROCESS module in SPSS. Due to SPSS and PROCESS being limited in the imputation methods - being unable to handle multiple imputation - the other...

02 March 2021 4,362 1 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Can NFL theorem be valid in infinite search space in ML?

NFL theorem is valid for algorithms training in fixed training set. However, the general characteristic of algorithms in expanded or open dataset has not been proved yet. Could you show your...

01 March 2021 1,189 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

How to arrange coordinates and extract climate dataset out of MPI-ESM-MR netcdf files?

Have a nice day everyone, I'm stuck in extracting datasets out of MPI-ESM-MR netcdf files because the latitude ranges from -3*10^6 to 3*10^6 and longitude ranges -5,9*10^6 to 5,9*10^6. Plus, the...

28 February 2021 912 3 View