Marwa Abd El Kader Zaater

15 Questions 26 Answers 0 Followers

Questions related from Marwa Abd El Kader Zaater

How can I simulate a metalloprotein-ligand complex in GROMACS?

I was wondering what changes should I add in the MDS protocol to account for the Zn ion in the active site of a metalloprotein. Also, I would be grateful if there was a bash script available to...

26 April 2023 2,805 2 View

How can I edit this non-peak line in 1H-NMR chart using Mestrenova?

I got this 1H NMR chart for a compound and I was told that the line I circled in red is not from the sample, however I don't know if there's a method to adjust that in Mestrenova. Any advice and...

24 March 2023 6,361 9 View

Can one predict the formation or not of Deep Eutectic Solvent (DES) from MD results?

I want to predict whether a certain molecular pair will form DES or not, is there one or more parameters that can be calculated from MD simulations from which I can know if this molecular pair...

08 June 2022 8,521 1 View

How to computationally predict water activity deviation from the Zdanovskii-Stokes-Robinson rule ?

I have some molecular pairs that formed deep eutectic solvents (DES) and others that did not. I want to be able to predict whether a molecular pair will form DES or not computationally. I found an...

07 June 2022 3,539 0 View

What are the limiting factors of ionic liquids formation?

I want to know what are the controlling factors that differentiate whether this ionic pairs are going to form ionic liquids or not, any help is highly appreciated.

31 January 2022 6,618 10 View

How can I plot the output of mdtraj.compute_dssp?

I used mdtraj.compute_dssp function to get information about the secondary structure attributed to each residue along my gromacs trajectory, however I don't know how to show that in an...

22 December 2021 7,748 2 View

How can I analyze the movement and stability of a certain secondary structure in a Gromacs trajectory?

I have a gromacs trajectory and I want to monitor the folding and stability of a certain helix in my protein, how can I do that? I tried to use DSSP through gromacs in version 2020.3, however on...

18 December 2021 7,948 3 View

How can I generate MD movie from a large gromacs trajectory?

I've a gromacs trajectory of 500 ns whose size after removing the solvent is about 2 GB. I want to generate a movie highlighting certain residues, I tried Chimera, it crashed and couldn't even...

21 November 2021 7,654 6 View

Does changing the -deffnm in a gromacs simulation restart (extension) give a complete extended trajectory with the newly set name ?

I am extending a gromacs simulation from 100ns to 500ns, if I used a different -deffnm file name, will the generated trajectory file be complete and extended (i.e. 500ns) or will it be as if it's...

22 October 2021 399 3 View

Does fourierspacing in gromacs MD simulation be the same for apoprotein and protein-ligand complex simulations?

I've run a simulation for an apoprotein using fourierspacing = 0.16, and I want to run a protein-ligand complex simulation (all using Amber ff). I found that it's suggested to set the value of...

25 August 2021 1,582 5 View

Does rlist have to be of the same value as rcoulomb and rvdw in gromacs mdp files?

I'm using Gromacs 2020 to run a protein ligand simulation using Amber99SB for protein and Amber (GAFF) for ligand, in the mdp files should rlist be of the same number as rcoulomb and rvdw e.g....

24 August 2021 5,690 2 View

What are the best free software tools that can predict in vivo pharmacokinetics parameters from in vitro dissolution data?

I have in vitro dissolution data for generic drug and I want to predict in vivo pharmacokinetics parameters, please suggest me free software tools or high quality R packages that can achieve this....

26 March 2020 8,089 1 View

How to rejoin a separated 2 chain protein after gromacs production run?

I want to know how to fix the separation of 2 chains after the production run. I'm trying different combinations of trajconv after creating an index file having a specific residue(s) on the...

13 February 2020 1,912 2 View

" db_createmolecule: Vector of wrong length" error in Multi Fragment Search tool in MOE software, how can I overcome this error?

I am using Multi Fragment Search tool in MOE software, when I try to load a fragment library other than the default one used I don't see the fragments to select in the selection pane of MFS...

05 April 2017 7,071 2 View

What tools are available to predict the transition of a protein from unstructured to structured in a trajectory?

I liked the idea of ANCHOR2 https://iupred2a.elte.hu/help of predicting the effect of binding of another structured protein to the disordered area, and I'm wondering if the same idea can be...

01 January 1970 8,787 3 View