18 Questions 49 Answers 0 Followers
Questions related from Sidra Rafi
I Want to download complete KEGG bacterial data please guide me how i can do that? or if any one have this data kindly send me. its not freely available for academic user too.
07 July 2019 9,011 6 View
Hi, I have a protein complex system, Initially i have minimized and equilibrate my system for 0.5ns. Then i want to slowly relax the side chain and back bone of my protein. i used all the restart...
10 October 2016 7,540 3 View
Hello, I want to know about umbrella sampling, and why it is required for potential of mean force for MD simulation?
09 September 2016 3,288 2 View
i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned...
08 August 2015 4,261 13 View
Hello, I am using Gromacs 4.5.6 version for protein ligand MD simulation. i completly follow Bevan La...
07 July 2015 6,791 9 View
Hello, I want to run protein ligand MD simulation using Amber99sb force field. i generated protein topology files using gromacs easily but when i generated ligand topology using AmberTools15 and...
06 June 2015 5,047 3 View
I want to calculate binding free energy of antigen-antibody complex after 30ns MD simulation. I used MMPBSA but it takes approx 12 days for 1 ns (500 frames) of antigen-antibody complex in which i...
02 February 2015 3,124 15 View
I downloaded PDB ID 4I3S it contains 16 missing residues in heavy chain of antibody as well as in antigen. I want to remodelled it before running the simulation. Which is the best computational...
11 November 2014 5,311 10 View
I want to calculate the half life of inter hydrogen bond of antigen and antibody. How I can do this?
07 July 2014 1,192 0 View
i want to calculate inter-hydrogen bonding between antigen and antibody using pymol. how i can calculate it and how i can get the hydrogen bonding log file?is there any way to get pymol log file...
06 June 2014 7,058 3 View
I have a plot in xvg format by using xmgrace and now I want to save it in pdf format. How can I do this?
05 May 2014 4,437 4 View
hello, can any one tell me the MD simulation analysis tutorial of protein-protein, peptide-peptide and ligand-peptide other than Bevan Lab tutorial. or if there any thesis related to it is...
03 March 2014 5,013 3 View
I want to calculate rmsf between both time and residues. Is there any way to calculate it using Gromacs?
03 March 2014 3,325 3 View
I ran antigen-antibody MD simulation of 100ns by using gromacs. I follow "Lysozyme in Water" Bevan Lab tutorial to performed simulation. My PDB structure contain 3 chains, chain A (antibody-light...
03 March 2014 5,485 5 View
I have 10ns antigen-antibody simulation tpr file . I want to make movie of it by using chimera but its having huge data so my computer get hang. Anybody tell me how I can make movie of it or how I...
03 March 2014 9,831 3 View
I have antigen as a protein and antibody as ligand, now I want to run this protein-protein simulation by using GROMACS. How can I prepare my antigen and antibody by Gromacs?
01 January 2014 7,360 5 View
I have downloaded 23 strains of Mycobacterium tuberculosis (M.tb). Now I want to know the country origin of all 23 M.tb strains. What is the shortest way to find it?
01 January 2014 3,777 2 View
I retrieved 100% identical significant alignment query and hits gene id by using SerachIO perl command but I did not get the complete name of that query and hit gi. How can I extract the complete...
12 December 2013 9,468 3 View
