Faez Iqbal Khan

11 Questions 34 Answers 0 Followers

Questions related from Faez Iqbal Khan

What does these Energy components of GROMACS suggested?

I calculated GROMACS Energy of a protein molecule using "gmx energy -f md.edr" command. I got Potential Energy, Kinetic Energy, Total Energy, Pressure, Volume, Density, Enthalpy, and Surface...

06 June 2016 5,285 7 View

What is the significance of "Number of residues Vs Time" secondary structure plot for a protein?

During secondary structure "Number of residues Vs Time" plot, I got these values; at 300 K: Average number of residues 136.7782 at 325 K: Average number of residues 151.2973 at 350 K: Average...

07 July 2015 1,679 5 View

How can I arrange atoms of my PDB file from CrystalMaker software?

Hi, I am performing MD simulations of ZnO nanocluster. I created nanocluster in Material Studio but atoms are not arranged. Can any1 help me to arrange the atoms in PDB file using CrystalMaker...

04 April 2015 2,616 3 View

Is anyone familiar with the trace of the covariance matrix and sum of the eigenvalues of a protein?

I am running "Principal Components Analysis (PCA)" for my protein at three different temperatures using "g_covar_mpi -s XXXXX.tpr -f XXXXXX.xtc". The results I am getting are : At 300 K: (1)...

03 March 2015 4,437 4 View

Regarding Reference temperature(ref_t) of MDP file of GROMACS?

There are two temperature in .mdp file of GROMACS. Can any1 suggest what they represent? If I want to use temperature range for MD simulation (300 K to 350 K), should I edit like this? ref_t = 300...

03 March 2015 8,335 3 View

How do I generate topology of a ligand using GROMACS and combine it with protein in a protein-ligand complex?

I am running MD simulation using GROMACS for protein-ligand complex. I used all the softwares (swissparam etc.) for ligand topology. I am always getting new and different errors. Can anybody...

02 February 2015 4,474 9 View

How to compare and Analyse "Hydrogen bond changes" between protein and its mutants during simulations?

I am running MD simulations of Protein and its reported mutants. I want to compare Hydrogen bond changes taking place between "one mutant and one protein". The commands I am using...

01 January 2015 10,017 3 View

Can anybody please help me to get titration curve of my my protein at different pH using MD Simulation?

I am running MD simulations at various pH using GROMACS. I used PDB file generated by H++ server. I want a good quality image of titration curve. please suggest if any softwares available?

12 December 2014 3,738 6 View

Can anyone help with a MD Simulation of Protein at different pH using GROMACS?

I am running MD simulations for my protein at different Temperatures using GROMACS packages. Can you please suggest me how to run MD at different pH with scripts?

09 September 2014 3,207 13 View

Generating ERROR while running MD SIMULATION on AMBER - any thoughts?

I am using this script running MD simulation on AMBER. #!/bin/bash#PBS -N eric.job#PBS -l select=1:ncpus=12:mpiprocs=12#PBS -l walltime=1:00:00#PBS -q kepla_k20#PBS -m be#PBS -o...

07 July 2014 8,153 8 View

How to run LEaP to generate the Amber MD simulations parameter and topology file for long chain amino acids protein?

I am running tleap for my 343 long chain amino acids. I can not generate any files. Please let me know what commands to use. Command i am using :...

06 June 2014 8,577 8 View