how can we decide on least energy structure of protein and ligand complex from MD simulation.
Run g_covar and we can get an average structure form it. Check this http://manual.gromacs.org/archive/4.6.7/online/g_covar.html
The wild type protein has shown no integer charge where as a mutation in protein R175H has produced an integer charge in system. I used pymol to mutate. is it the centre of problem. Help wil be...
03 April 2016 4,422 2 View
I want to test dihedral PCA for my mutated pocket and have trouble understanding the tutorial. How can i generate covar.ndx from the dihedral angles generated in before step. And regarding the...
03 April 2016 9,970 2 View
how can i renumber .gro and .top residue numbers to start with a specific number. The scenario is that i have first 40 residues of DNA and i dont want to disturb them. I just want to renumber from...
02 March 2016 571 1 View
I am finding it difficult to perform cationic dummy atom model for p53 protein. can anyone suggest me a good and little detailed procedure. * if i perform it with xleap program of ambertools14,...
01 February 2016 3,082 0 View
I am getting an error in xleap module of Ambertools 14 in which it is unable to find leaprc nor anyother file i added to respective folders as said in this tutorial...
01 February 2016 7,648 2 View
Molegro Virtual Docker is now little difficult to access and use so can any one please suggest better reliable software for template based LIGAND docking where a template of the ligand is made and...
09 October 2015 9,093 0 View
I tried to align molecules basically proteins at different frames to understand the ligand interaction. But to my dismay it shows an error "measure fit: selections must have the same number of...
08 September 2015 8,854 0 View
when ever i run a simulation in gromacs i end having a note saying GPU is 20% more in use than cpu which could decrease the performance and GPU/CPU ratio is 7.5 which should be ideally. Suggest me...
07 August 2015 2,634 0 View
i am a newbie to gromacs(molecular dynamics software), please help me out. i compiled gromacs 5.0.2 for mac and successfully done installing it. But when i checked the following command mdrun...
05 June 2015 2,670 4 View
I have performed series of modelling experiments using modeller to get a series of modeller proteins. But here i am unable to produce models with good GA341 score. I have a hundred percent match...
02 March 2015 6,188 9 View
How to develop investments in renewable energy sources?
08 August 2024 5,112 3 View
I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...
07 August 2024 505 3 View
why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...
03 August 2024 3,589 3 View
I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...
03 August 2024 1,370 1 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC
01 August 2024 967 3 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...
30 July 2024 9,824 2 View
Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer
30 July 2024 3,354 1 View