Aswin Abbas

6 Questions 9 Answers 0 Followers

Questions related from Aswin Abbas

Error in ONIOM with variation layer of Amber in gaussian.

I had make made ONIOM input file from PDB file used 2 layers i.e. B3LYP/6-311++G(2d,2p): AMBER, but I don't know why it always get error (error message: "aborted....", "segmentation violation")....

01 January 1970 3,543 3 View

MM function not complete in ONIOM

I have ONIOM file which consist of two layer i.e. High Layer (HL) and Low Layer (LL). HL was adjusted for 5 amino acid residues and LL for rest of residues. When I run in Gaussian09, I got failure...

01 January 1970 9,896 2 View

Make input file in ONIOM.

Hi, I did docking process to find out the active site of recector molecule then I want to optimize the result using ONIOM in gaussian 09. How can I make input file in ONIOM from the result of...

01 January 1970 2,557 8 View

How to find the value of scoring in Vina?

Hi, I did a docking between protein and ligand using Autodock Vina. In terminal, I try to run and I got three variables i.e. Energi, rmsd l.b., and rmsd u.b. . 1. What is difference between...

01 January 1970 1,626 2 View

What are differences among chain A, chain B, and chain C in molecular docking?

Hi, I'm a beginner in molecular docking. I want to know what the purpose of chosen just one chain in docking process? how to determine the most influential binding site of amino acid residue of...

01 January 1970 4,992 8 View

Error in running PDB file using ONIOM

I docked one ligand to one protein then I got the best mode of ligand and I combined the ligand best mode to the protein in PDB file. I carried out ONIOM for next step but I got error such as...

01 January 1970 5,187 1 View