In which file i can find c alpha atoms for my protein in between GROMACS files?
how to study a certain type of mutations with another type of protein (not mutation and totally different from mutation) by (bioinformatics tools). What is your opinion and suggestion about this?
05 June 2019 4,401 2 View
i want study cancer genome by bioinformatics tools. can advice me in articles or review paper can guide me to do my research.
03 April 2019 5,164 5 View
What kind of scientific research ( hypothesis ) can I do and complete it in the absence of availability or absence possibilities to do this research. Knowing the research I want to do is related...
08 September 2018 6,374 5 View
I want to study of 3D protein structure (contact map) with complex networks, calculate the centralities of C alpha atoms, specially those atoms of the amino acids, in which software or tools can ?
09 October 2015 9,055 2 View
i run MD simulations with GROMACS for my protein and i want to know is it my simulations converged. How to know that ,how i will do it and confirm ?
09 October 2015 8,375 1 View
Im trying to run x.pdb file but when select force field it give Error(Residue not found).already tried different force field but keep same error. what can to do to solve this error?
08 September 2015 6,685 7 View
Im using molecular dynamics to study stabilization of protein at low pH but when am checking by VMD it shows no any salt bridges also I was used different software like gromacs salt bridges but...
05 June 2015 8,199 5 View
I want to know n terminus and c terminus for protein but according to molecular dynamics simulations by gromacs especially in (RMSF).
11 December 2014 6,275 3 View
i need to know mutations can effect on protein backbone ,protein folding,secondary structure ?
08 September 2014 3,397 0 View
I did molecular dynamics simulations for different mutations and I want to compare how hydrogen bonds effects on stability and the other properties of mutations.
05 June 2014 5,447 3 View
If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...
07 August 2024 5,343 2 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...
07 August 2024 8,414 2 View
Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...
06 August 2024 1,989 3 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...
05 August 2024 6,787 4 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
If from a geometric perspective the non-halogens, non-noble gases have more empty spots in their valence shell, and the filling/exiting of any of the empty spots in the shell constitutes a...
03 August 2024 4,787 2 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
If you think of electrons with spin as bar magnets, you know bar magnets of opposite polarity as long as they're not occupying the same spatial location don't cancel out each other's magnetic...
03 August 2024 3,927 2 View