Ayesha Fatima

9 Questions 10 Answers 0 Followers

Questions related from Ayesha Fatima

Cholesterol simulation in gromacs?

Dear all, I have tried everything on the smiling list to simulate the cholesterol membrane. but nothing seems to work. The error is grompp NO default proper dihedrals, no default UB types. Since...

10 October 2019 5,089 2 View

Cholesterol simulation gromacs?

Dear all I have been trying to simulate a cholesterol membrane built with the charmm membrane builder in gromacs 2019. I have tried using various forcefields to start wit the first step of...

09 September 2019 4,868 5 View

Pull code in Gromacs 2019?

Hi all, I am getting this error my gromacs steered dynamics simulation. When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the...

02 February 2019 6,730 2 View

Docking with chimera?

Hello everyone. I am interested in using the builtin vina docking tool in Chimera. However, i get stuck at the same point. Errno 13:Permission denied "dock.receptor.pdb". I have gone through...

11 November 2017 5,907 2 View

How do you run a QM/MM using Amber?

I am trying to run a QM/MM in Amber on a protein-ligand system. I have looked for tutorials but they don't explain a few things such as how to heat your system and equilibrate it before MD. Then...

10 October 2014 7,205 3 View

Does anyone have experience with multiple ligand simulation?

Hi. I am trying to check whether multiple copies of the same ligand can bind in a stable conformation to a protein. I know many people have done this but I can't find the exact protocol. I have...

09 September 2014 6,829 5 View

Does anybody have experience with ligand binding selectivity in Molecular Dynamics (MD)?

I working with a ligand that has shown an affinity towards a certain protein. I am interested in knowing its natural binding site using MD. Any suggestions or advice?

01 January 2014 6,524 3 View

Studying ligand selectivity of a binding pocket: How to determine the most probable target?

I am studying a small molecule that has several reported targets. Can anyone guide me how to determine which is the most probable target? I have done docking studies and screened the targets based...

01 January 2014 7,378 0 View

help on proteins

Hi, I am new to the group. I am looking for some material on developing a new method for detecting enzyme inhibition at molecular level. the enzyme is a cell surface protein. it is highly expressed.

05 May 2010 2,404 3 View