Nithyanan Annamalai

4 Questions 2 Answers 0 Followers

Questions related from Nithyanan Annamalai

Fatal error when using pdbgmx to run NRAS bound with GTP using GROMACS 4.6.7?

I have tried to run simulation for protein complex of NRAS(5UHV) bound with Mg and GTP. However I have encountered the following error while using pdb2gmx: Program pdb2gmx, VERSION...

19 December 2019 2,360 3 View

How to do SNP detection for exon short read sequence (.ab1 and .seq file format) obtained through Sanger sequencin?

Hi, I am a newbie learning to do SNP detection using exon reads of Chromosome 17 obtained from Sanger sequencing. I have tried to use the GATK workflow: BWA-0.7.12 (alignment) PICARD-0.1.119...

28 January 2016 5,590 8 View

What is the standard method to perform insilico mutagenesis?

I have performed in silico mutation using VMD. But I need explanation on : a.) How to manage NTER and CTER? Do we need to change the charge or cap it or do nothing to it? And if we do need to...

29 July 2015 9,784 4 View

What is the importance of the shape and size of the simulation box in a molecular dynamic simulation?

How do we can determine the shape and size of simulation box in GROMACS that suites best for the target protein? Does the wrong box shape will have effect on final results of a simulation?

14 May 2015 2,802 4 View