Debanjan Saha

6 Questions 6 Answers 0 Followers

Questions related from Debanjan Saha

What is the values in terms of energy of electrostatic intrctns, van der Waals intrctns, H-bond, hydrophobic intrctns in protein-ligand binding?

Among the above interactions which is more important and why?

24 December 2024 3,953 2 View

Query reagarding yeast t-RNA MD simulation?

I am using Gromacs 2020.4 for MD simulation study of yeast t-RNA (PDB ID- 6TNA) but the force field parameter file(rna.rtp) does not have CM atom charge values for adenine and guanine atom types....

14 February 2023 6,370 2 View

What are the + and - sign indicate in different properties of Admetsar online server?

There are different properties present in Admetsar 2.0 version to calculate admet of molecules. But the output values and sign doesn't clearly represent what it actually means.

18 October 2021 427 3 View

How to download the SMILES of all compounds in a batch from PubChem?

I am trying to download all the smiles of a similar structure of a particular compound from PubChem.

12 October 2021 6,100 4 View

Using Open Babel, I am getting warnings during conversion of 2D SDF to 3D PDB ?

I am using this following code babel -i sdf *.sdf -o pdb > *.pdb --gen3D I got warnings like 3D coordinate generation failed Errors/Warnings *** Open Babel Warning in CorrectStereoAtoms...

09 September 2021 6,775 4 View

Query regarding Raccoon?

I have installed the tool Raccoon in ubuntu. I was able to open it and load ligands, receptors , grid and dpf files successfully. However, I could not able the run the command ./RunVS.sh as it...

27 June 2021 761 0 View