Dr Rajesh B Patil

5 Questions 36 Answers 0 Followers

Questions related from Dr Rajesh B Patil

How to get the contact map between two protein chains from gromacs trajectories?

I am seeking a way to obtain the contact map between two chains in a protein post MD simulation in gromacs. The objective is to analyze and know which residues in two chains are important during MD.

02 February 2022 574 3 View

Is anyone using BRAF facility of C-DAC Pune for MD with Gromacs?

I am trying to submit the MD production phase job on BRAF C-DAC server for which I have compiled newer version of Gromacs (5.1.2) through my login. I can also use old version of Gromacs 4.5.6...

19 March 2019 2,371 0 View

Topology from mol2 file

I want to generate a top file for a MD simulation in Gromacs. I specifically want all atom topology. The ATB server indeed generated such topology, but I want to use Amber charges loaded in mol2...

17 March 2014 3,223 9 View

Energy minimization?

Gaussian 03 can perform energy minimization by applying various basis sets like DFT/B3LYP level 19 and using the cc-pVDZ. Which other free software can carry out similar types of optimization?

08 January 2014 6,746 14 View

Is anyone familiar with the reaction of 1,3-benzodioxole, derivative of 7,8-dihydroxy coumarin?

I have tried the 2-substituted 1,3-benzodioxole derivative of daphnetin (7,8-dihydroxycoumarin) by literature methods of 2-substituted 1,3-benzodioxoles of catechol and aromatic acids. I have...

21 October 2013 5,311 1 View