Harindu Rajapaksha

10 Questions 17 Answers 0 Followers

Questions related from Harindu Rajapaksha

Does any one know the binding residues of human ACE2 which interact with the spike protein of Covid-19 ?

I want to find the residues of human ACE 2 which interact with the spike protein of Covid-19? or can anyone tell me a method to find the interaction residue for this PDB file? PBD ID: 6lzg thank...

11 April 2020 3,041 5 View

What are the methods that can be used study adsorption by using Gaussian.?

Dear sir/ madam I am studying about filtration of pesticides. how can I study the adsorption pesticides to the filtering medium using DFT in Gaussian 09. I have already tired using homo lumu...

07 June 2019 2,542 2 View

How to make a PDB file with the receptor and ligand from docking results from autodock.?

I have docked a ligand with a perticular receptor and obtained the most stable 10 binding place. i need to visualize the binding site using pymol and i only can input pdb files to pymol. how can i...

30 May 2019 1,893 6 View

Where can i find the structure file of polyacrylamide to be using in Gaussian to study it's properties ?

I am hopping to use the structure file to study of polyacrylamide to study its homo lumo levels using DFT in gaussian 09w and to use the structure in molecular mechanics to study the adsorption...

27 May 2019 4,736 4 View

What is the best CPU for running Gromacs and Gaussian ?

Hello everyone. I am planning to build a workstation capable of running both gaussian and gromacs. I have planing to use RTX 3080 as the GPU and 64GB memory. However, I have not able to select a...

01 January 1970 7,304 2 View

Why do i get a convergence error in gaussina DFT calculations eventhough the stationary state is found during geometry opt ?

Dear sir/madam, what is the reason for the above mentioned observation ? How can I eliminate it ? Thank you

01 January 1970 4,951 6 View

How to validate and refine Protein structure (PDB cystalography data) ?

I am planing to do a docking analysis of protein 3VW6 using autodock. how can i validate and refine the crystallography structure ? I found these two web site claming to do so. can these sites...

01 January 1970 6,125 2 View

The NAMD2.exe fails to startup. How can I overcome this problem ?

I have tried all the suggestions on the internet but failed to correct the above error. The application was unable to start correctly (0xc000007b) can someone tell me how to overcome this...

01 January 1970 8,783 5 View

What is the best online server to generate images of the ligand - protein interation with publicantion quality ?

For example, to generate an images like the one which I have attaced

01 January 1970 7,569 23 View

What is the most suitable basic set (DFT) for heavy metals such as Hg, Pb, Cd, Cr, Ni and etc ?

I am looking for a reliable basic set for heavy metals up to the 6th row. I am looking forward to carrying out these calculations using gaussian 09. What is the most suitable basic set for my...

01 January 1970 5,635 13 View