Dr Rajesh B Patil

12 Questions 74 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 656 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 2,431 0 View

How to dock few ligands with multiple receptors using autodock vina?

How to carry out docking of few ligands againt set of multiple receptors using aurodock vina. Is any python script available to do this?

03 November 2018 4,295 15 View

Can PLS regression in QSAR be handled by R?

There are number of programs which can do PLS regression in QSAR study but these are commercial. I am looking for some R codes which can do PLS regression in stepwise manner i.e. variable...

14 April 2018 3,854 4 View

Anyone using Self-organizing Molecular Field Analysis (SOMFA) in their research work?

SOMFA is used to derive the relationship between structre & biological activity of compound. May be this program has become obsolate as it is not used by anyone recently. Somewhere I read that...

26 April 2017 5,663 2 View

Can anyone suggest freeware for virtual screening?

Through 3D QSAR and docking studies in autodock vina we have hypothesized a pharmacophore. We want to screen few databases for this pharmacophore and propose the hits or novel classes of hits....

21 April 2015 2,123 5 View

Can anyone suggest how to write a Bash script for making complexes of ligands and receptor?

I am working with autodock vina for virtual screening and docking. Autodock vina generates conformers for multiple ligands. I want to make the complex of these conformers with receptor. e.g. I...

17 January 2015 2,618 3 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 3,283 9 View

How to fund the remainder of my research?

The current funding for my research project has dried up. Any suggestions where do I get short funding for rest of my project? Project involves design, synthesis and pharmacological evaluation of...

12 March 2014 1,437 4 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 6,812 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 5,371 1 View

How to justify my rationale for Tyrosine kinase inhibitors through docking?

I am doing my work on chromenones. I have proposed them as anticancers and antiinflammatory agents in my preliminary protocol. I chose Protein Tyrosine kinase (EGFR) as a target (PDB: 1m17 & 4HJO)...

27 August 2013 4,969 8 View