22 Questions 19 Answers 0 Followers
Questions related from Vigneshwaran Kannan
I have been reading the following article on peptide structure prediction. https://www.biorxiv.org/content/10.1101/2022.02.17.480937v1.abstract I wanted to know whether alpha fold 2 can be used to...
20 June 2023 7,070 6 View
I was using fragbuilder module in python to generate peptides of sizes 4, 6, and 10. However, the issue with fragbuilder module is that some of the bond angles are deviating from the standard...
23 May 2023 3,665 4 View
I have lots of pdb files of short peptides of size 18. I tried with dssp. But the issue with dssp in mdtraj module is that it misses the beta strand compeltely as a single strand does not have...
21 May 2023 5,739 0 View
I require the generation of peptide structures and computation of van der Waal interactions (1-4 interactions) from a given set of backbone Ramachandran angles, for fixed bond lengths and bond...
05 March 2023 3,016 5 View
I generated a large number of peptide structures for a given sequence using the peptide builder module. However, the peptide builder module does not include hydrogen atoms all along the peptides....
16 February 2023 583 1 View
I have a set of Ramachandran angles. I wish to make Ramachandran plot out of it with standard allowed region contours in the background in Python. I couldn't do that in python. If not in python,...
04 November 2021 7,335 3 View
I need to download multiple PDB files (more than 300 pdb files) from PDB data bank and to read Ramachandran angles of specific residues in each PDB file. How could I do that in python? If not in...
25 October 2021 5,410 4 View
I have come across the following word end capping in pentapeptides. Does it mean fixing the Ramachandran angles of end amino acids?
04 October 2021 6,544 4 View
In page number 255 amber manual 2020, it has been mentioned that value (under the figure number Figure 14.2) of Rmin of carbon is mentioned as 1.908 A. However, the image shows the value (in the...
13 May 2021 5,195 2 View
I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...
01 February 2021 7,255 3 View
I want to read out the partial charges of N terminus amino acid and C terminus amino acid. I checked with AMBER. It has N terminus amino acid files and C terminus amino acid files for all the...
26 January 2021 3,990 4 View
I am a beginner in the field of molecular dynamics and biochemistry. I need the parameters such as van der Waal radii, partial charge of each amino acid. How do I read directly the parameters from...
21 January 2021 3,673 3 View
I built short peptides in Avagadro, using Build--->insert--->peptide. After constructing the short peptides of 4 amino acids(tetrapeptide). Under the drop-down, View--->Atomic...
28 December 2020 895 3 View
I have been reading this paper. https://cnx.org/resources/9c9fe5128dfef772b498990a94c49df16c4f09ee/transformation_derivations.pdf Here, they have computed for forwarding kinematics to compute...
19 October 2020 8,349 3 View
I am trying to plot the following points in VMD. It is plotting as points. However, It is not connecting the points from A to B to C to D to E to F to H by a line. How do I do it? If not in VMD,...
16 September 2020 4,358 3 View
I have been reading the following (open access) journal, In this paper, they have collected data samples from the loop region and categorically classified into TURN, COIL and BRIDGE, 3-10 helix...
11 September 2020 4,122 4 View
I am trying to write down the slater determinant for 10 electron filling from 1s up , 1s down, 2s up, 2s down, 2px up, 2px down, 2py up,2py down, 2pz up, 2pz down, There are totally 10 single...
17 July 2019 6,249 1 View
Is it really possible to give multiple input blocks in a single file ? Can ORCA recognize it as separate input and run them separately and produce the output for multiple inputs
29 March 2019 1,985 6 View
While solving for the molecular hamiltonian in ORCA. What command I should use in ORCA to ignore the electron electron repulsion term in the molecular Hamiltonian. Is it possible to make print the...
02 March 2019 3,654 1 View
Suppose there are n particles in 3 dimension space coupled to one another via harmonic oscillator potential. Is it possible to solve it quantum mechanically exactly in closed form ? Kindly someone...
19 April 2018 3,267 2 View
For the Hamiltonian , H=hw (a*a). How could one evaluate the green's function in the path integral approach using coherent states for a fermion (or boson) ? In particular, one can evaluate this in...
16 May 2017 8,240 1 View
For a given hamiltonian H=-J∑SiSj -h∑SI in the one dimensional ising model, small h and capital J are applied magnetic field and strength of nearest neighbor interaction.Now how to evaluate...
13 May 2017 5,150 3 View
