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Questions related to Molecular Dynamics Simulation
These are the most controversial thesis of the famous physicist. Most of the community disagree but no official thesis yet (i m working on one) partly because no big journal published them. The...
05 March 2023 8,212 18 View
I want to retain crystallographic waters in protein structure while docking a ligand. How to prepare pdbqt file in Vina considering explicit waters? Also is there any modification required in the...
05 March 2023 2,325 2 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 3,139 5 View
I'm planning to do some molecular dynamic simulation with Gaussian, (trying to simulate the alignment of an ensemble of water molecules in the presence of strong field), can anyone please explain...
03 March 2023 2,296 3 View
I have made a membrane + protein system in Charmm gui can you give me methods to "how to do analysis on membrane protein computationaly?"
02 March 2023 5,160 4 View
My stock protein concentration is 2.13mg/ml. I have to have a final concentration of 0.83 nanomoles and my final volume for the protein would be 50 microlitres. The molecular weight of the protein...
01 March 2023 5,553 3 View
I have the output (-out.cms) file of the protein ligand simulation from Desmond. I wish to analyse some different aspects of the obtained Desmond output file in Gromacs. What are the necessary...
28 February 2023 9,851 0 View
How to prepare topology file for coordination (complex) compounds. Topology files for organic ligand molecules can be obtained using online servers such as SwissParam and etc. How to prepare a...
27 February 2023 4,057 1 View
I want to use cpptraj for some analysis but I need to convert my topology and trajectory files from Gromacs xtc, tpr format to Amber nc and parm formats. Could you please let me know how can I...
26 February 2023 3,141 2 View
I created a file af polycrystal diamond using atomsk and saved it using .lmp extension. When I run the file in lammps it is unable to read it but when I prepare a .lmp file for single crystal...
23 February 2023 2,110 3 View
I need to store a large amount of MD simulation trajectories in a database that I can interact with using python. Do databases like this exist currently?
22 February 2023 5,058 2 View
Hello, I am trying to apply a restraint between an atom in my ligand (atom number 12) and an atom in the active site of my protein (atom number 582) in GROMACS. I have modified the [ bonds ]...
16 February 2023 9,115 2 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 720 1 View
I obtained protein-ligand complex using AutoDock and i would like to visualize 2D Plot Protein-Ligand (coordination compound, co-crystals) Interactions for the complex. But, only one part of...
15 February 2023 8,780 0 View
I am doing a simulation of a solvated box where I need to confined the ions within the volume of the box, I tried applying flat bottom position restrain in x,y,z directions and that did not work...
15 February 2023 4,329 4 View
If we are using IOp in Gaussian, for which functionals we can use the IOps?
10 February 2023 9,738 1 View
Can somebody please suggest the best tool to view, model and edit 3D protein structures at no cost?
09 February 2023 677 12 View
I was wondering if someone could clear up the difference between domain decomposition in GROMACS and LAMMPS. As I understand it LAMMPS creates ghost atom copies of atoms in surrounding domains and...
08 February 2023 9,141 0 View
Hello! I have performed umbrella sampling to study the covalent bond formation between a ligand and a Cysteine residue. Where Histidine is a proton-donating residue to complete a reaction. I have...
08 February 2023 4,909 1 View
I am adding the Graph result below. The whole trajectory run was 20 ns. is there any particular threshold value for H-bond?
08 February 2023 9,454 2 View
sir/madam can anyone suggest the physical unit of Fukui function in Density functional theory calculations
08 February 2023 3,914 2 View
If estrogen is not exogenously given, can MCF7 cells grow into tumors under the skin of female nude mice?
07 February 2023 10,068 2 View
I want to determine the interaction energy between the MgO surface and polymer coating using Materials Studio software. What should be (h k l) cleave plane to have a cut-off distance of at least...
06 February 2023 6,421 1 View
Dear all, I am currently working on the simulation study of a complex whose ligand cannot be automatically parameterized. I have been using AMBER to do the parameterization, and now I have...
03 February 2023 430 2 View