Amit Kumar

6 Questions 13 Answers 0 Followers

Questions related from Amit Kumar

Why phosphodiester bond is formed at 3' carbon in RNA predominantly?

Hi Everyone! I am little curious to understand the nucleotide polymerization concept. My confusion is that, generally, the phosphate group is attached to the 3' of ribose sugar. But there are...

08 April 2025 7,833 1 View

Is it possible to regain the topol.top file from tpr file?

Dear Sir, I am using gromacs and have mistakenly deleted topol.top and topol_Protein_Chain_*.itp files after running the simulation. But I need those files for calculating Interaction Energy and...

29 June 2020 5,146 0 View

Can anyone tell me why gromacs 4.5.5 is not generating data (not showing any error)?

Hi Everyone, I am trying to run REMD in implicit solvent using gromacs 4.5.5, where I am not getting output or any data file except a log file containing only developers' information. So, I am...

28 February 2020 9,445 4 View

How can I calculate configurational entropy along the complete trajectory of gromacs?

gmx anaeig calculates configurational entropy of the system. But it does give only one value of entropy. Is there any option I can use for calculating entropy along the complete trajectory?

03 February 2020 1,485 8 View

Why I am getting this error while installing Gromacs4.5.5?

I was trying to install gromacs4.5.5. I have followed the tutorial http://www.gromacs.org/Documentation/Installation_Instructions_4.5.5 using fftw3.1 and automake, openmpi. When I was using...

03 January 2020 5,343 0 View

I am simulating a protein in Gromacs in implicit solvent. But I am getting few errors. I tried some changes but nothing happened. Can you help?

This is the input file for equilibration. title = NVT Equilibration ; Run parameters integrator = sd ; leap-frog integrator nsteps = 250000 ; 2 * 50000 = 100...

22 November 2019 7,262 7 View