Saman Yousuf Ali

9 Questions 15 Answers 0 Followers

Questions related from Saman Yousuf Ali

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...

11 November 2016 1,491 3 View

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...

11 November 2016 4,615 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 ...

08 August 2016 4,792 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...

07 July 2016 9,585 12 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...

01 January 2016 1,919 2 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...

01 January 2016 777 1 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...

12 December 2015 7,191 3 View

NAMD tuitorial for Membrane Bound Protein Complex Structure.

Can anyone tell me the link of NAMD tuitorial for Membrane Bound Protein Complex Structure?

04 April 2015 6,908 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...

01 January 2015 2,077 3 View