Ibrahim A Osman

23 Questions 18 Answers 0 Followers

Questions related from Ibrahim A Osman

How to study mutations with another type of protein by bioinformatics tools?

how to study a certain type of mutations with another type of protein (not mutation and totally different from mutation) by (bioinformatics tools). What is your opinion and suggestion about this?

06 June 2019 4,347 2 View

How to cancer genome analysis by bioinformatics tools?

i want study cancer genome by bioinformatics tools. can advice me in articles or review paper can guide me to do my research.

04 April 2019 5,110 5 View

Absence of availability or absence possibilities to do biological and medical science ?

What kind of scientific research ( hypothesis ) can I do and complete it in the absence of availability or absence possibilities to do this research. Knowing the research I want to do is related...

09 September 2018 6,232 5 View

How simulations converged?

i run MD simulations with GROMACS for my protein and i want to know is it my simulations converged. How to know that ,how i will do it and confirm ?

10 October 2015 8,322 1 View

Which tools and software to study of 3D protein structure (contact map) with complex networks?

I want to study of 3D protein structure (contact map) with complex networks, calculate the centralities of C alpha atoms, specially those atoms of the amino acids, in which software or tools can ?

10 October 2015 8,998 2 View

C alpha atoms GROMACS?

In which file i can find c alpha atoms for my protein in between GROMACS files?

10 October 2015 8,654 0 View

What would the reason be for residue not found when start to run simulations with Gromacs?

Im trying to run x.pdb file but when select force field it give Error(Residue not found).already tried different force field but keep same error. what can to do to solve this error?

09 September 2015 6,625 7 View

Anyone familiar with modeling salt bridges at low pH?

Im using molecular dynamics to study stabilization of protein at low pH but when am checking by VMD it shows no any salt bridges also I was used different software like gromacs salt bridges but...

06 June 2015 8,147 5 View

How to determine n terminus and c terminus in molecular dynamics by gromacs?

I want to know n terminus and c terminus for protein but according to molecular dynamics simulations by gromacs especially in (RMSF).

12 December 2014 6,226 3 View

PROTEIN FOLDING & MUTATIONS

i need to know mutations can effect on protein backbone ,protein folding,secondary structure ?

09 September 2014 3,350 0 View

Can anyone help me with how to analyze the effecting of hydrogen bonds?

I did molecular dynamics simulations for different mutations and I want to compare how hydrogen bonds effects on stability and the other properties of mutations.

06 June 2014 5,399 3 View

I have pqr file and I want to do a run for it in gromacs. How can I do a run (commands)?

05 May 2014 1,473 0 View

How can I install an APBS plugin to pymol?

Please can any researcher can help me to install an APBS plugin to pymol because i have download it but do not know how to add to pymol.

04 April 2014 1,948 6 View

Can anyone help with confirming a protein was protonated with pdb2gmx?

How can I confirm the protein was protonated with pdb2gmx commands. It will be protonated at ph that I need to run simulation with it (ex 2.4).

04 April 2014 3,274 4 View

How can I change the protonation state of some of my protein residues to mimic different pHs in Gromacs?

I'm trying to study my protein in different pH conditions (using Gromacs) but how can I change the protonation state of some residues of my protein to mimic different pH? I have already used H++...

04 April 2014 9,276 3 View

Is anyone familiar with studying hydrophobicity and hydrophilicity with Gromacs?

I want study the hydrophobicity and hydrophilicity with Gromacs and I need to know how to calculate both and their effects on my protein.

03 March 2014 9,934 3 View

Can anyone help with salt bridges with gromacs?

I used this command to know the salt bridges in my protein g_saltbr -f md.trr -s md.tpr but how do I show the graphs and other details for salt bridges with gromacs?

03 March 2014 831 5 View

Does anyone have experience with RMSF & DSSP Gromacs?

I did my simulation for protein with gromacs the result of RMSF was show flacutaions in protein structure in different area but the DSSP it does not show any change in structure. Why did this happen?

03 March 2014 955 2 View

Is anyone familiar with different proteins from different organisms that have the same pathogens?

I have found two different proteins from different organisms that have the same pathogens and make the same diseases. There is no similarity in sequence. How can I study their properties...

02 February 2014 9,677 1 View

How can analysis and interpret RMSF graph results for Gromacs ?

I did my run simulations for protein but I want know how to analysis my results (rmsf).

02 February 2014 1,893 6 View

Can someone advise on Gromacs simulation (pressure) and (temperature)?

I am seeking to use diverse (pressure) with diverse (temperature) in gromacs but I need to know what changes can I do with (md,pr,em) files and if possible if can tell me a good manual or method...

01 January 2014 9,376 3 View

How can you determine the percentages of secondary structures of protein?

I want to know the percentages of secondary structure for my protein that I have already done simulation on with GROMACS but I need the commands for the percentages.

01 January 2014 2,073 7 View

I'm using gromacs to study dynamics of (prion) protein. How do I change parameters to (500k) without blowing up?

I do with (300k) but when increasing temperature (400,500 k) blowing up. I changed parameters many times but got the same results

12 December 2013 6,577 4 View