Mohamed Shehata

11 Questions 22 Answers 0 Followers

Questions related from Mohamed Shehata

How to create a coarse grained model of a protein and ethanol using martini forcefield ?

I want to create a coarse grained model of a protein solvated in ethanol box. I could do that with water by using charm-GUI and VMD but with non standard solvent it seems complicated. any suggestions?

02 February 2020 1,597 2 View

How to use polarizable force fileds like Drude in NAMD ?

As stated in NAMD tutorial it is presently beyond the capability of the Psfgen tool to generate the PSF file needed to perform a simulation using the Drude model. So how can we generate suitable...

06 June 2019 6,580 1 View

In NAMD, should the flexible cell option turned on during NPT simulation ?

I am confused about setting the cell basis in NAMD. Initially, I set the cell basis according to my solvation box dimensions + 2 or 3A to separate the unit cells in the PBC. This is fine during ...

05 May 2019 8,840 5 View

How can I calculate the torsion angles of a specific residue side chain over MD trajectory in VMD?

I performed a 100 ns MD of a protein in an organic solvent and I want to calculate the change in torsion angles of a specific residue side chain over the simulation. is there any script to do that ?

07 July 2018 1,653 1 View

Namd OR Gromacs?

I have been using NAMD for one year now and I haven't used GROMACS yet. For those who used both of them, which one is more efficient?

05 May 2018 9,321 2 View

What is the best concentration to study the effect of an organic solvent on enzyme?

I am studying the effect of different organic solvents on lipase stability. To compare the wild-type enzyme with it's mutants in terms of stability, should I work at very drastic conditions like...

03 March 2018 2,401 5 View

How can an organic solvent improve an enzyme activity ?

It has been known that most of the organic solvents have a detrimental effects on enzymes activity and structure but, if incubation of an enzyme in a specific organic solvent lead to an increase...

03 March 2018 5,786 6 View

How can I run a repetition of MD simulation using NAMD ?

I performed a 50 ns production simulation for a protein in an organic solvents using NAMD. Now I want tp run a repetition for the simulation. I read about different approaches but I confused. can...

02 February 2018 1,982 7 View

SEM analysis of an immobilized enzyme on Eupergit C 250 L

I am going to carry out SEM analysis for my immobilized enzyme ( Alcohol dehydrogenase) on Eupergit C 250 L (epoxy-polymer). Any recommendation or precautions during sample preparation process?

06 June 2017 3,469 1 View

Using Bradford assay at very low protein concentration ?

Actually I am immobilizing my Enzyme ( an alcohol dehydrogenase ) on Eupergit C 250 L . In order to determine the amount of enzyme that didn't bind to my matrix , I use Bradford assay to...

04 April 2016 3,835 6 View

How do large proteins fold?

i mean is there any difference between the folding mechanism of large proteins and small ones ?

11 November 2014 1,313 4 View