Aritra Bej

4 Questions 10 Answers 0 Followers

Questions related from Aritra Bej

How can you generate a homology model from two or more structural segments?

I am trying to build the model of a protein using homology modeling. The available structures of the protein are partial. Specifically, the available structures are of specific domains/segments of...

16 October 2020 5,534 13 View

How can I model a 60 residues loop region?

I am working with a trans-membrane protein that I have modeled by homology modelling. In all predicted structures, the trans-membrane part have been modeled nicely. But I face problem with the...

13 May 2015 8,794 6 View

What is the Y-axis depicted exactly during calculation of RMSD distribution using "g_cluster" of Gromacs Package?

During calculation of RMSD distribution using "g_cluster", the Y axis of the XVG file denotes a.u. i.e arbitrary unit which I think probably the frequency. But it is not clear which frequency it...

16 April 2015 5,758 1 View

How can one retain any HETATM (eg. - Water, Lipid, Ion) in Coarse-grained model?

I am going to use MARTINI force field. According to the MARTINI tutorial (http://md.chem.rug.nl/cgmartini/index.php/proteins), I am trying to convert my atomistic protein model to CG model using...

30 June 2014 9,511 1 View