9 Questions 24 Answers 0 Followers
Questions related from Uddipta Ghosh Dastidar
In post-MD analysis of Biomolecular systems, we often determine the suitable Free Energy LANDSCAPE & Free Energy SURFACE. Is there any difference between the two? Or just different names of the...
18 June 2025 3,408 0 View
I performed MD of a protein-ligand complex in Gromacs. I generated the RMSD curve using this command. · gmx rms -f traj.xtc -s md.tpr -n index.ndx -tu ns -o rmsd.xvg Least square fit: Backbone...
24 May 2025 8,952 1 View
For MD Simulation of proteins, how many nanoseconds is appropriate? Is 100ns is ok? Can I reduce it for smaller proteins? Does it depend upon the Residue number of proteins and Nature of proteins?
26 November 2024 2,354 3 View
Although we mostly join the backbone gaps in the protein before starting a MD Simulation, longer gaps (more than 10 residues) are sometimes difficult to join. If we conduct MD Simulation without...
20 November 2024 9,624 2 View
I use Discovery Studio for Small Molecule docking. I want to export those docked complexes in Schrodinger Maestro Academic, and generate corresponding Docking Scores. Is it possible?
11 September 2024 9,065 3 View
I have an active small molecule inhibitor of an enzyme. The S enantiomer has IC50 0.5 µM. The R enantiomer has IC50 1.1 µM. But the racemic has IC50 2.4 µM (i.e. less active than both R and...
11 May 2023 1,622 6 View
In the LigPrep module of Schrodinger Maestro, using EPIK, several ionization states are generated for a single molecule. To choose among them according to ionization penalty values, are the states...
21 February 2023 9,858 0 View
I am using GROMACS 5.1.5, for MD simulation of a dimeric protein to study the gradual separation of two chains. However, in certain frames (as seen in VMD) the chains are suddenly completely...
01 December 2022 4,415 9 View
I have a homodimeric protein (Chain A & B) in complex with two same ligands (LIG1 & LIG2) for MD simulation in Gromacs. I have created separate ITP files for both ligands and the MD has completed....
01 December 2022 6,588 6 View