Debanjan Saha

4 Questions 4 Answers 0 Followers

Questions related from Debanjan Saha

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 6,335 2 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 6,055 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 6,718 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 726 0 View