Uddipta Ghosh Dastidar

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Questions related from Uddipta Ghosh Dastidar

Free Energy LANDSCAPE & Free Energy SURFACE : What is the difference?

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 3,414 0 View

How to perform Free Energy Landscape analysis using RMSD and Rg instead of PC1 and PC2 in GROMACS?

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 8,961 1 View

Gmx_MMPBSA: Why Interaction Entropy curve always start from Zero (0 kcal/mol)?

I ran MD of a Prot-Lig complex for 200ns. Then proceeded to GBSA calculation using gmx_MMPBSA. Start frame = 0 and Endframe = 20000; interval = 50 (in mmpba.in) The entropy curve for the full...

06 February 2025 5,879 0 View

How to choose appropriate time for MD Simulation? 100ns or 500ns: How to decide?

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 2,360 3 View

MD Simulation of Proteins with small residue gaps in backbone: Is it OK?

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 9,631 2 View

What are the optimal ADME parameter values of a Small molecule Vaccine Adjuvant?

I have developed a small molecule intended to be used as a vaccine adjuvant. What are the ideal and acceptable values of 1. LogD, 2. Human LIver Metabolism (HLM), 3. Mouse LIver Metabolism...

04 October 2024 537 0 View

ΔG value is positive in gmxMMGBSA for my best active compound. What it signifies?

I performed post-MD MMGBSA for one of my best active compounds (IC50: 2 nM). But the ΔG value is positive. What can be the reason? a. Is the MD simulation time not sufficient? (But the ligand is...

26 September 2024 812 1 View

Can I generate Docking Scores in Academic Maestro using docked complexes, obtained from another software?

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 9,072 3 View

Why the Biological Activity (IC50) of my Racemic molecule is greater than both of its individual pure enantiomeric components?

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 1,639 6 View

EPIK Ionization Penalty in Schrodinger Maestro: Less or More; Which is favourable?

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 9,871 0 View

Why in GROMACS MD, proteins chains are separating suddenly instead of gradual shifting?

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 4,422 9 View

How to index two same ligands separately, attached with two chains of dimeric protein in Gromacs for MD simulation?

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 6,593 6 View