Manoj Patel

7 Questions 9 Answers 0 Followers

Questions related from Manoj Patel

How does histone bind to plasmid-DNA in cytoplasm?

someone please explain what is the nature of histone binding to plasmid DNA in CYTOPLASM 1) Does histone bind in form of nucleosome to plasmid? or they float in the cytoplasm as individual...

28 September 2023 3,848 2 View

Why martini for DNA says "This is a beta of Martini-nucleotide and should NOT be used for production runs."?

I am trying to coarse-grain nucleic acid chain usng martini tutorial. Whicle doing so ther is message which says "This is a beta of Martini-nucleotide and should NOT be used for production...

06 February 2023 2,589 1 View

How can I apply soft potential to remove overlapping atoms in GROMACS?

Hi I have a martini system of 1642 atoms. Most of them are overlapping. I tried running energy minimization with all sorts of parameter manipulation but system doesn't resolve and crashes. I am...

25 January 2023 9,525 1 View

Which Proteins are responsible for protein-DNA compaction?

Hi I have certain queries regarding plasmid-DNA transport inside the cell and would be glad if anyone could help me out. 1) As we know there are several proteins/components, which bind DNA...

19 January 2023 8,778 5 View

Why can't see I "open in local terminal" option in llinux distros other than ubuntu?

I tried ubuntu and many other Linux distros. In ubuntu when I open the file browser of a remote machine and when I am in any remote directory, the mouse right-click in file explorer empty space...

02 September 2022 1,280 2 View

How to build topology file of unknown residue/molecule?

Hi I need to build psf of m7G capped rna structure (pdb id-6IS0). The m7G is unrecognizable by topology file. Can anyone please help me in building psf of this whole structure. I can't find...

17 July 2022 5,805 2 View

How to fix clashes/overlaps of atoms in pdb file?

Hi I downloaded pdb file from rcsb and fixed missing residues by using Modeller. Now I have full dequence of pdb but few of the residue atoms are clashing with other backbone residues. How can I...

01 January 1970 8,684 7 View