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Questions related from Seshank Mutya
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...
04 April 2016 4,398 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...
04 April 2016 9,943 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...
03 March 2016 540 1 View
how can we decide on least energy structure of protein and ligand complex from MD simulation.
02 February 2016 5,336 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,...
02 February 2016 3,025 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...
02 February 2016 7,589 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...
10 October 2015 9,063 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...
09 September 2015 8,804 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...
08 August 2015 2,601 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...
06 June 2015 2,642 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...
03 March 2015 6,152 9 View
is it actually possible to see the binding energy poisson-boltzmann surface of a receptor and ligand binding site. When i was uploading the ligand i was facing an error saying cannot convert the...
03 March 2015 5,502 0 View
I was assigning color by properties in PYTHON MOLECULAR VIEWER. I assigned temperature factor in it. Now i am unable to understand what it actually signifies. Could any one explain it elaborately?
03 March 2015 4,644 0 View
I have attached an image and want to know what does the colour of spheres indicate ( for example the red sphere) and what probable things should I be searching while analyzing my results. Explain...
02 February 2015 4,609 7 View
i have docked few molecules in to same receptor but could'nt judge which ligand is best...i just have just affinity (kcal/mol). is that enough? with that how can i judge the molecule. And also if...
02 February 2015 2,223 5 View
