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Questions related to Molecular Dynamics Simulation
I have the free energy landscape data how do i get this??
28 May 2023 5,133 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 5,385 0 View
my work on molecular docking, pharmacokinetics, DFT KINDLY SUGGEST
27 May 2023 3,041 1 View
I need to use the AutoDock program, but I tried both versions 1.5.6 and 1.5.7. I had no problem loading, my only problem is that when I open the program, the loading remains around 9% in the...
23 May 2023 6,116 3 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 3,678 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 5,755 0 View
Hello everyone, I am trying to determine relative expression values for specific genes in different life-stages of my organisms (adult, larval, and microfilaria). For each of the three...
11 May 2023 5,224 3 View
During spectroscopic analysis of paclitaxal order from sigma, I am getting the maximum absorption of paclitaxal dissolved in methanol at 211 nm. However, according to the previously reported...
09 May 2023 6,312 2 View
Hello every body , I want to know how can i insert my coordinate of orbitals en tight binding model at Pythb formate. thanks in advance
09 May 2023 8,256 0 View
I am trying to determine some mechanical properties of Hf-Nb-Ta-Zr high entropy alloy. But I'm not being able to relax it properly & it's causing absurd values of elastic moduli,...
08 May 2023 6,179 1 View
Hi all, I am trying to use the BFEE plugin in VMD to calculate the free energy of a protein-ligand complex. However, I keep getting the error below when I try to generate the input...
08 May 2023 9,618 0 View
My first Edited book titled "Indian Tourism: Diaspora Perspective" by Emerald Publishing has been indexed in Scopus. While I'm happy, I'm intrigued to know on what basis, the books are selected...
04 May 2023 8,564 3 View
The box size determined for my protein before starting the MD simulation is as in image 1. After 200 ns, some of the protein comes out of the box (image 2). Does this affect the simulation...
03 May 2023 3,908 3 View
After running of python script downloaded from MacKerell lab website a file is generated: ligand_ini.pdb. After viewing it in VMD it does not look like the ligand any more.There is no error in...
03 May 2023 3,114 2 View
Can an MD simulation be performed by adding other salts by varying their concentration inside the box?
02 May 2023 9,210 3 View
I have attached the output file. Please help me.
01 May 2023 3,056 9 View
Hello, I'm interested in surface reaction mechanism. So I read some papers about this. There are two types of papers. 1.DFT calculation(VASP) using NEB method 2.Chemkin mechanism calculation I...
01 May 2023 4,049 0 View
I'm a windows 11 user and I am having problems launching autodock tools 1.5.6 and 1.5.7. The GUI will just launch up to 6-8% and then it will crash and will not continue opening. I already tried...
28 April 2023 1,400 4 View
Hi is there any way to extract intra-molecular distance distribution in a cluster of geometrically optimized cluster of molecules in Gaussian?
27 April 2023 791 2 View
My protein of interest is fused with MBP tag, and it does not contain tryptophan but MBP does. After factor Xa digestion, my protein was separated from MBP, and I eluted my protein while MBP is...
25 April 2023 1,145 2 View
why ligand is getting detached from protein at the complex.gro step when I am generating the ligand toplogy from ATB , swissparam, acpype serverserver? while this problem did not occur while using...
24 April 2023 8,580 1 View
I am performing an all-atom molecular dynamic simulation in LAMMPS to perform the diffusion and adsorption capacities of gaseous hydrogen in metal alloys. For the simulation, I am using an...
24 April 2023 6,545 4 View
After refining the protein structure multiple times, it still fails to pass VERIFY3D. The ERRAT score is 96.9298 and PROCHECK results are fine. What can be done to improve the VERIFY3D results?
24 April 2023 6,720 3 View
I'm working on a virtual screen of approximately 8000 compounds, and I need to select only those that interact specifically with an active site residue. However, it is clearly impossible to...
24 April 2023 9,689 0 View