The RMSD trajectory for bare protein and protein-ligand complex almost coincides and cannot diffrentiate. What is the reason behind it?

More Suraj Pukhrambam's questions See All

How to select target material for X-Ray generation?

Generally, the target material is Mo, Co, Cu, Fe, Cr, etc, so on what basis should we choose this material?

31 July 2024 5,824 0 View

Dengue in Southern states in India?

There is rapid surge of dengue cases in Southern parts of India. However there are no cases till now in the setting I work in Northern India. Besides dengue surveillance and local preventive...

14 July 2024 2,935 2 View

What is the scaling factor for DFT/B3LYP/6-311++g(d,p) level of theory for optimization and frequency analysis?

I have read some papers but i didn't get proper answers. In some cases, my level of theory is not exactly written. I will be very gladfull for any recommendation

10 June 2024 9,929 1 View

Why did the color of the liquid electrolyte become Yellowish instead of a colorless solution?

I am using the liquid electrolyte EC:DMMP(50:50 wt%) mixed upto 1M LiTFS. Usually, the electrolyte obtained was colorless ...but the Last two times, it gave a yellowish color. Why?

01 June 2024 8,355 1 View

How to run DFT calculation using Gaussian 09 in a GPU, window?

I have intel iris xe graphic card. i want to run dft calculation in gaussian using a gpu. what are the necessary modifications to the input file? my input file read like...

21 May 2024 3,402 6 View

Water Surveillance in field setting ?

If we get a unsatisfactory water report from water supply from a locality? What preventive measures should be taken in already scarce water situation?

27 April 2024 851 0 View

How to calculate exact 75% germination time using formula?

I have collected data from the field in consecutive days. I have those data in excel how can i calculate the exact day of 75% seed germination using any formula.

17 April 2024 1,077 3 View

RO water and loss of minerals?

We are witnessing silent epidemic of Vitamin D deficiency in India. Any solution to problem of RO water and loss of minerals?

10 April 2024 4,716 0 View

Rising number of mumps cases in India?

We are witnessing rising incidence of mumps . Adults are also getting complicated mumps in form of orchitis. Any reasons to explain?

07 April 2024 8,983 0 View

CHARMM was terminated abnormally?

while trying to generate CGenFF topology for Ligand after extracting from docked file, i got error which i'm showing as a picture. What could be the possible reason and how will i rectify it for...

26 March 2024 2,491 3 View

Can we analyse RMSD for peptide-HLA docking and binding affinity for peptide-HLA to TCR docking, in a peptide-HLA-TCR docking ?

In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?

11 July 2024 4,831 0 View

In silico techniques for identification of inhibitor/activator/substrate activity?

Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...

08 July 2024 4,724 4 View

RMSD of Protein ligand complex is higher than the apo form.Why?

I have performed a 100 ns md simulation for protein ligand complex .The result generated is found that the complex RMSD is higher than the Apo form.What could be reason for this ? Could anyone...

24 June 2024 9,049 3 View

What could be the possible reason of a sudden fluctuation in a stable RMSD plot of a protein-protein simulation?

I have run MD simulation of a protein-protein docked complex for 50ns. The RMSD plot obtained from the simulation is attached here. The RMSD plot shows a stable trajectory for entire simulation,...

09 June 2024 7,886 1 View

Comparison of three-dimensional structures obtained in Swiss-Model?

Good day! Please tell me, is it correct to compare two structures obtained using homology modelling on the SwissModel website and then compare them using RMSD in PyMOL?

18 May 2024 3,566 1 View

RMSD plot from GROMACS output file .xtc did not start from 0ns. How to get the 0ns frame?

Dear GROMACS expert, I am currently having trouble to analyse the results from my simulations. After processing the output files using this command, gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o...

02 May 2024 6,690 7 View

What is the best practices and presentation for analysis of multiple molecular dynamics simulations ?

Hi, I've noticed a common practice in publications where multiple Molecular Dynamics (MD) simulations are conducted with varying initial velocities. However, I'm uncertain about the appropriate...

18 April 2024 6,293 2 View

Reason(s) for the difference in RMSD of the Docked Structure and Co-crystal?

Aside from defining the disulfide bond, what other reasons could account for the significant difference in RMSD of the docked structure and co-crystal?

15 April 2024 7,706 2 View

How do I split my Autodock Vina pdbqt file into indiviadual comformation files on windows?

I want to calculate the RMSD for the individual confrmations from the output file pdbqt into to run in into a program that only accepts PDB files. I can convert pdbqt files to PDB using openbabel...

25 March 2024 3,075 5 View

VMD NAMD Plot?

Hello. How can I plot in RMSD H-Bond and radious gyrus in VMD in Windows? I ran MD in Namd and y I have all the files Step5.

23 March 2024 7,689 1 View

Jobin Thomas

You can do one thing....

try to take snapshots at different time points of trajectory to verify that the protein is intact or not within the protein.....

Sometimes if the ligand is out of the simulation box.... the trajectory will be as same as bare protein.....

Regards

Suraj Pukhrambam

when i play the simulation, the ligand is in intact within the protein, also i don't see the simulation box. what shall i do then?