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Questions related from Marwa Abd El Kader Zaater
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 2,817 2 View
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 6,369 9 View
Reported procedures mainly use fuming nitric acid (concentration >86 %) with or without conc. H2SO4 to nitrate quinazolineones, however the only available concentration for me is 69%, can it...
12 June 2022 7,012 1 View
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 8,532 1 View
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 3,549 0 View
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 6,631 10 View
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 7,757 2 View
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 7,962 3 View
I was recording an MD movie in chimera and I used the following per frame script to show H- bonds: findhbond linewidth 2 color yellow selRestrict cross reveal true I then got this error after...
10 December 2021 6,458 2 View
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 7,671 6 View
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 413 3 View
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 1,594 5 View
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 5,702 2 View
LeadOp+R: Structure-Based Lead Optimization With Synthetic A... I want to try this algorithm, but can't find a downloadable link or any data regarding its access and usage conditions, any help...
11 June 2021 7,084 1 View
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 8,103 1 View
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 1,924 2 View
We noticed that in many formulas, Lactose and Avicel are used together, not necessarily in their co-processed form, I mean their simple individual mixing, what effect do they have on each other...
16 January 2019 298 10 View
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 7,083 2 View
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 8,800 3 View
I was wondering what makes a researcher interested to read and respond to an email sent from another researcher (they don't know) asking for a collaboration? In your opinion what would you like to...
01 January 1970 2,274 0 View
