Simran Modi

4 Questions 4 Answers 0 Followers

Questions related from Simran Modi

Amber ligand parameterization error?

I have been trying several methods to parameterize the acetyl Coa ligand using both the web-based i.e charmm gui, playmolecule, cgenff method and antechamber method of Amber. The ligand...

02 August 2024 3,255 3 View

Not able to give GAFF forcefield to my ligand?

I have been able to assign the CHARMM forcefield to my ligand i.e. acetyl coenzyme A but not the amber forcefield. I want to run amber forcefield and the parameterization of ligand is failing. I...

16 July 2024 7,500 1 View

Error in CHARM GUI Solution Builder?

I have input the pdb file combining both protein and ligand in it and I am getting this error repeatedly. Kindly help me with this.

08 July 2024 9,043 2 View

While doing docking using Autodock1.5.7, I am getting a warning that there are non integral charges on my ligand. How to remove it?

I used Autodock for docking, due to the non integral charges on my ligand I am not able to dock with the protein. How to dock the file?

09 June 2024 5,662 2 View