Vikash Kumar

5 Questions 48 Answers 0 Followers

Questions related from Vikash Kumar

Should we raise voice agianst misuse of Journals Impact factors?

Over the past few years impact factor has become the sole evaluation criteria for the Scientific research. It is now aggressively used for the recruitment of scientists, teaching faculties and for...

06 June 2015 7,631 1 View

Can anyone advise me on a problem with phosphoserine residue in MD simulation?

I am working with a protein having phosphorylated serine residue. During topology generation in Gromacs I faced this problem with the above mentioned residue. Please suggest a forcefield, which...

01 January 2014 9,404 2 View

Can coarse grained molecular dynamics (CGMD) simulation be applied to study Protein Interaction stability?

I am working with a system consisting of two protein molecules. My aim is to predict the stability of complex through molecular dynamics.

09 September 2013 8,746 2 View

Diffrence in calculated binding free energy by MMPBSA.py and mm_pbsa.pl

I have calculated binding free energy of two proteins using both MMPBSA.py and mm_pbsa.pl script.I am using 500 frames generated during 1ns simualation under NPT condition.In case of MMPBSA.py i...

04 April 2013 2,491 0 View

Problem with Amber Parameter generation of Protein containing Mg+2 AND GTP

I am getting an error about bond and angle parameter of MG -O-P5 in Amber. I don't know how Mg ion is treated along with GTP in protein complex. I have generated separate parameters for GTP and...

04 April 2013 9,534 0 View