Maham Hamid

9 Questions 5 Answers 0 Followers

Questions related from Maham Hamid

Can replicates of energy minimization have same potential energy?

I have energy minimized my structure using gromacs for 20 ps following the lysozyme tutorial. I did 3 such replicates for the minimization. The potential energy for all these 3 replicates was the...

06 May 2024 7,770 4 View

Edit trajectory based on RMSD?

I have calculated the RMSD. I want to edit the trajectory such that all those frames that have an RMSD value greater than a threshold are saved in a separate trajectory. Can anyone help me with this?

21 March 2024 7,615 1 View

Understanding Gmx gangle ?

I have a protein and I want to check the orientation of side chain of a particular resdiue A with respect to the residue B in the active site. any help on this regard? currently I am using gmx...

23 February 2024 3,913 2 View

Hbonds in protein trajectory?

i have a 10 ns simualtion of protein. I want to perform H bond analysis where I can get the number of H bonds that are form between residue number 10 - 50 in each frame. such that I get separate...

18 February 2024 1,149 4 View

Protein conformation during 10 ns simulations in gromacs ?

I have modified the protein and I am simulating it using GROMACS. I have performed the 20 ns simulation after energy minimization and during visualization in VMD I observed that a few frames have...

13 February 2024 6,001 4 View

RMSD after energy Minimization ?

I have a modified protein and I am following the Gromacs tutorial to simulate it. I have been asked to visualize the RMSD vs Time plot for the protein before the preproduction run. the energy...

07 February 2024 437 3 View

Missing carbon group in Tryptophan in protein structure prediction?

I predicted a protein structure using trRosetta. I couldn't do homology modeling as no homologs are present. the model contains tryptophan but the indol group of tryptophan lacks one carbon. (...

26 September 2023 9,923 1 View

What predicted protein model to use?

Dear All, I am trying to predict the structure of a protein ( 700+ amino acid). I have used different servers including I-tasser, alphafold , raptorX, etc. but couldn't get good results. I have a...

06 September 2023 9,633 3 View

What parameter and topology files one should use to model water molecules that are present in the pdb structure?

I want to perform MD simulation on a protein that contains water molecules in PDB what forcefield parameters (topology/ parameter ) files should one use ?

27 March 2023 5,775 5 View