Mahesh Kumar Velusamy

9 Questions 27 Answers 0 Followers

Questions related from Mahesh Kumar Velusamy

Does anybody knows how to convert Charmm 22 DIHR values to amber format?

Dear All, We are working on parametrization of x non-standard (NR) residue using Charmm22, GLYCAM 06 (amber format) and GAFF force fields. Among these, we can able to parametrize them...

16 October 2017 6,094 3 View

What is a method for understanding the molecular mechanism of protein X?

In a case where we carried out a genetic Screening of genes that involved in the stress response in E. coli. From this screen we identified a gene that encodes a 50 kDa flexible protein (Protein...

14 November 2016 4,872 4 View

How to generate a topology file for structures that has covalent bond (link between RESIDUE and Ligand) in GROMACS?

Dear All, I have tried to build topology file for a structure that has covalent bond (Between ligand and protein) by using pdb2gmx with the following command: pdb2gmx -f WILD0MODEL.B99990001.pdb...

18 August 2016 9,576 6 View

How to generate a model with double mutant & combination of mutants by using mutate_model.py ?

Dear All, I hope you all know that default mutate_model.py script works only for single mutation but I want to make it for double and combination of mutation and I beleive this would be possible...

09 June 2016 7,014 1 View

How to optimize & refine the conformation of the mutant side chain along with the backbone by using modeller (mutate_model.py ) ?

I hope you all know that there is script available in modeller "mutate_model.py". To generate a mutant models and then optimize the mutated residue following refinement in sidechain alone but I...

03 June 2016 1,710 3 View

Is there any external tool avail for calculate DOPE score alone?

Actually, I generated 5 models by using modeller and done side chain repacking on it by RASP (RApid Side-chain Predictor). Now, I want to validate side chain repacked models by comparing DOPE...

01 September 2015 6,938 1 View

How to get all the conformations which are mentioned in number of modes by using Autodock vina?

We have experimental data for two ligands, we are trying to fit this data with Autodock vina results so we can increase the weightage of Hydrogen bond and Hydrophobic interactions. Here our main...

03 December 2013 2,854 16 View

Can anyone tell me that how to prepare input file (SDA structure file with Activity data) for QSAR studies?

How to get SD file (structure associate with activity data) of cdk2 inhibitor?

04 October 2013 1,419 0 View

Is there any insilico technique to define the best ligand for wet lab experiments after molecular docking?

I'm currently trying to find Molecular targets by using Molecular docking (Autodock vina). Now am having only the lowest binding energy with comparative (Cocrystal ligand - ligand) poses. I would...

16 September 2013 1,033 11 View