Madhusudan Dutta

7 Questions 16 Answers 0 Followers

Questions related from Madhusudan Dutta

How to solve "KeyError: 'NL' Exiting. All files have been retained" problem during gmx_MMPBSA run?

I have simulated a protein-ligand complex by using gromacs software and gromos 54A7 force field was deployed for this purpose. Ligand topology (.itp) file was prepared by usimg ATB server. Now...

29 October 2021 4,255 3 View

Can I use gmx_MMPBSA with the trajectory that has been created by using gromos 54A7 forcefield?

I have simulated a protein-ligand complex by using gromacs software and gromos 54A7 force field was deployed for this purpose. Ligand topology (.itp) file was prepared by usimg ATB server. Now my...

27 October 2021 1,554 5 View

How to see atomic contacts between residues by gromacs?

After performing md simulation I want to see the atomic contacts between residues. For that I have performed gmx mdmat and followed by gmx xpm2ps by using following commands gmx mdmat -f...

10 October 2021 6,941 4 View

Why Gabedit 2.5.0 is unable to read the .com file which was extracted from gaussian .log file?

By using Gaussian 09 I have optimized a molecular structure. By this process a .log file has been generated. Now I want to extract the converged structure by using Gabedit 2.5.0. for which I have...

27 November 2019 2,534 1 View

Which company/brand provides good quality Hexafluoro-2-propanol in India?

I need Hexafluoro-2-propanol or Hexafluoroisopropanol for SPECTROSCOPIC study of beta-amyloid (a very costly item). Unfortunately I can't see Hexafluoro-2-propanol (liquid) in Sigma-Aldrich. So I...

09 August 2019 6,332 2 View

How to build topology file of small molecule without using ATB or PRODRG?

I want to run a MD of a protein in presence of a small molecule by using gomacs software also want to apply GROMOS 53A6 forcefield. But parametrization is a problem for me. I have already tried...

25 November 2016 7,696 3 View

How may I determine the concentration of β-amyloid (1-42)?

I dissolved 0.1 mg of β-amyloid (1-42) in 0.1 ml of HFIP. After evaporation of HFIP by speedvac further it was dissolved in 1X PBS buffer (concentration= approximately 22 μM ). But when I was...

26 November 2014 3,776 20 View