Ashutosh Shandilya

3 Questions 13 Answers 0 Followers

Questions related from Ashutosh Shandilya

Is there any way to go towards a native structure of a modelled protein when the native structure is not known?

Generally any model structure is 6-8 angstrom from native when there is low similarity but for drug designer it is not helpful. Is there any way to get a better structure at least lower rmsd when...

12 December 2012 6,425 2 View

How can one make topology file( gro file) for small molecules using amber force field in gromacs

is there any server which uses amber force field to make gro file. acpype commnad can convert amber topology to gromacs. If theres another direct way to deal with this

11 November 2012 7,564 7 View

Most of the time it is observed that RMSD increases during heating in MD simulation even with the crystal structures. Why? Is it right?

I want to simulate a modeled protein which is around 7 angstrom from native and I want to see whether it goes towards the native with time. What could be the parameters so that the protein does...

11 November 2012 4,412 18 View