Najme Dehghanbanadaki

11 Questions 14 Answers 0 Followers

Questions related from Najme Dehghanbanadaki

What is the problem with removing PBC from my trajectory?

Dear all, I performed a simulation of a membrane-transporter and ligand for 50ns. During the simulation, and as I expected, the ligand comes out of the transporter protein and does not come back....

08 February 2024 1,516 3 View

How can I calculate PCA for a particular domain of a protein simulated using Gromacs?

I simulated a 600 a.a receptor containing two separate 300 a.a domains in complex with three different ligands. I want to calculate and compare the collective motion of each domain in these three...

10 August 2020 6,223 2 View

Is Amber03 a reasonable force field to simulate protein structures and dynamics?

I performed a molecular dynamics simulation for a peptide-receptor complex using the Amber03 forcefield and TIP3 water model. The simulation is convergent in 50ns. Based on the Amber tutorial,...

06 April 2020 4,136 4 View

How can I define a palmitoyl in Amber force field using gromacs program?

Hi every one. I have a protein with a palmitoyl bound to it with a esteric bond(palmitoyl OH group bound to OH group of a amino acid serin). does any one have a similar experience? any help will...

06 February 2017 1,982 4 View

Dose any one know a docking sofware to define the isotype of an element?

I have a peptide, coordinates to an isotope of nitrogen. how could i keep the isotope in the docking procedure?Any help will be appreciatedbest regards.

25 November 2016 1,566 3 View

How could I get a protein sequence from uniprot using matlab?

Hi i work on a bioinformatic project about ebola virus, i need to have the protein sequence of about 1000 viruses but i have just they uniprot id. how could i get theire sequences from the web...

26 July 2015 6,500 4 View

How can I set the pressure in NPT phase of molecular dynamic simulation?

We could set temperature with kinetic energy in MD. How about pressure in NPT phase?

20 January 2015 8,880 7 View

How should I treat the peptide with the cells?

The following is written in the article below: (A) Cancer cells in 6-well plates were treated with mouse pept ( 2 mM), human peptide (4 mM) or control peptide (4 mM) in a medium containing 2% FBS...

29 June 2014 8,375 6 View

Can anyone help with modelling a hetero dimer using modeler?

I have a complex, a receptor, and a ligand. The ligand is a short peptide. I want to make a model of the complex using a modeler program. How should I make the aln.file? I used the online...

29 June 2014 2,865 1 View

Can anyone help me to find the force constant of a special bonds in Gaussian?

I have problems with calculation of the interested bonds force constants in Gaussian output file. I searched the freq-output file of my project and just found this string "Internal Coordinate...

17 June 2014 8,227 9 View

Can anyone help regarding insulin as a growth supplement for culturing HS578T cell line?

I don't have access to bovine insulin which used add the protocol of cell culture. I want to use human insulin for the culture so I have three question: first, has anyone used human insulin for...

26 May 2014 4,685 5 View