13 Questions 38 Answers 0 Followers
Questions related from Sidra Rafi
Hi, I want to calculate dock6 amber scoring function of multiple ligands (i.e. 15000). i follow the below tutorial http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm i faced...
23 September 2019 363 1 View
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.
02 July 2019 5,723 6 View
Hi, I performed 70ns MD simulation of protein system. Now I want to find hydrogen bond of specific atom of protein during the whole simulation. i want to know that specific atom makes interaction...
01 February 2017 615 14 View
Hi, I have download a crystal structure having 8 missing residues in it. I build these missing residues using modeler missing residue script but it ignored my all water atom. i add one line in...
25 October 2016 8,231 5 View
Hello, I am using autodock4 for blind docking of ligand-protein.the size of protein is very large, its contain 5 domains. now i want to make large grid box that cover the whole macro-molecule but...
20 May 2016 7,786 8 View
i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned...
01 August 2015 1,012 12 View
Hello, I am using Gromacs 4.5.6 version for protein ligand MD simulation. i completly follow Bevan La...
07 July 2015 2,601 8 View
hello, I want to calculate RMSD of docked multi ligand with a protein using MOE. Please can you suggest how I can calculate this?
04 March 2015 3,763 8 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...
19 February 2015 359 14 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...
25 November 2014 6,604 9 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...
25 June 2014 5,391 3 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...
06 March 2014 1,562 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...
24 December 2013 8,854 2 View
