48 Questions 29 Answers 0 Followers
Questions related from Vigneshwaran Kannan
Can someone clarify whether the Pymol version is available in GitHub free or to be subscribed to? Can this Pymol be installed in Python and be used for research publications ? I installed Pymol...
13 June 2024 10,056 2 View
I have a large number of peptides. Is it possible to save a peptide structure in Pymol in PNG formally without having any extra spaces around it? I am using Pymol in Python to save the peptide PDB...
23 April 2024 5,946 4 View
I want to cluster multiple pdb files with respect to one reference pdb. I have to use Align > all this to *Ca in Pymol. However, how could i do this via scripting in Pymol? As I have multiple...
16 October 2023 10,141 3 View
How to show two peptide structures side by side on Pymol. I have 100 PDB files. I want to show all the 3D image structures side side in a two-dimensional array form. How could I do the same in Pymol?
15 October 2023 8,258 6 View
I have a collection (around 500) of peptide 3D structures (PDB file each 10 residues long and for a given sequence). I need to cluster it based on RMSD values among them. Is there any Python...
09 August 2023 6,203 2 View
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 7,161 6 View
I wanted to have a rough estimate on time it takes to get the complete thermal distributions of backbone Ramchandran angles of a given peptide size of 18. Is it possible to estimate the time...
30 May 2023 673 1 View
I wanted to know whether DSSP assignment hold good for peptide sturctures of size 10 and 18. I have large number of pdb files of peptides of various sequences and of size 6, 10 and 18. Can DSSP...
28 May 2023 5,452 0 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 3,739 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 5,824 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 3,096 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 668 1 View
I want to know why one needs to align two different protein molecules before computing RMSD. Is it because of the fact that both molecules are in different frames of reference and the respective...
15 June 2022 8,570 0 View
I am calculating the van der Waal interactions between atoms in the PDB file python. As this interaction does not involve bonded atoms and the atoms which are two bonds away (1-3 atoms) along the...
04 June 2022 2,305 0 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 7,391 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 5,467 4 View
If MD simulations converges to Boltzmann distributions ρ∼exp(−βϵ) after sufficiently long time why do we need MD simulations, as all the macroscopic quantities can be computed from the Boltzmann...
10 October 2021 5,618 2 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 6,652 4 View
Will it be useful and helpful to do MD simulations of 5 amino acid sequences? What do we infer if we do MD simulations for such a system. Short peptides do not have any unique structure. Can we...
05 August 2021 1,441 0 View
I have seen the below attached work has made freely available the Ramachandran distributions for dipeptide. Similar to this I need to know whether there is any other database which provides...
30 June 2021 4,298 0 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 5,295 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 7,416 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 4,066 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 3,814 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 1,029 3 View
I want to minimize the Lennard Jones Potential and charged electrostatic potential for a tetrapeptide. However, as the parameters like epsilon and partial charges are not the same for different...
15 December 2020 1,441 0 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 8,573 3 View
How alpha 1 helix is different from alpha 2 helix. I have been reading the following paper in which they mention in Figure 1 of page 9. Alpha helix one region corresponds to (-70,-30) and alpha 2...
18 September 2020 3,816 0 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 4,473 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 4,247 4 View
I couldn't understand, how Ramachandran did the Ramachandran diagram for protein. In general, all the interactions are electrostatic, which is in fact long range, then how Ramachandran did the...
02 August 2019 2,151 0 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 6,340 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 2,292 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 3,716 1 View
I am trying to solve a hamiltonian with 10 nuclear centers with Z=1 and located in arbitrary locations (assumed no symmetry in its arrangement). For the the given set set (classical ) nuclear...
25 February 2019 9,899 2 View
I am trying to solve a hamiltonian of an electron moving in the presence of 10 (Z=1) nuclear centres located in three dimensional place(locations are quite random and there is no symmetry in its...
15 February 2019 1,350 4 View
I am trying to solve numerically Helium atom problem (spectrum of two electrons with interaction with nucleus and electronic repulsion).. I have excluded the kinetic term of nucleus and put the...
18 October 2018 7,971 0 View
I wrote a C program to produce cartesian coordinates of a protein molecule, with internal coordinates (bond angles, bond lengths,ramachandran angles as input). I have not included side chains and...
09 August 2018 7,694 3 View
Can someone suggest a good reference wherein I can find a way to quantize vibrations of protien molecule .?
08 May 2018 2,734 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 3,370 2 View
I am trying to solve the pseudo harmonic oscillator in the following paper. They have used laplace transform to solve the eigen value problem. However, the Energy eigenvalues look strange as I am...
26 December 2017 8,664 0 View
To get to know about the structure of the Ramachandran angles and Ramachandran plot, Why don't we need more than two torsional angles. ? What restricts it to just two ?
17 November 2017 7,966 0 View
I am reading the paper on, "Entanglement Entropy and Quantum Field Theory"https://arxiv.org/pdf/hep-th/0405152.pdf In this paper, the author introduces cut in the path integral which is referred...
02 August 2017 689 1 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 8,296 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 5,264 3 View
How to evaluate the critical exponents of modified van der Waals equatioThe given modified van der Waals equation is (P+(a/v)n)(v−b)=RTwhere (n>1). What is the physical significance of the...
13 May 2017 7,963 1 View
how to evaluate a finite product exp(-w*ti) where t is the time axis and i runs from 1 to N-1 with tN-1 =T and t1=0.What do we get if we send N to infinity and and length of each slice of time to...
30 April 2017 6,837 1 View
It is easy to evaluate the green's function using path integral approach by evaluating classical action and using functional calculus method. Is it possible to evaluate path integral for harmonic...
23 April 2017 2,503 4 View
