01 January 2015 3 10K Report

I am running MD simulations of Protein and its reported mutants. I want to compare Hydrogen bond changes taking place between "one mutant and one protein".

The commands I am using are:

(1)make_ndx_mpi –f md.gro –o faez.ndx

(2)r382

(3)g_hbond_mpi –f md_noPBC.xtc –s md.tpr –n faez.ndx –num hbond.xvg –nonitacc

I got list of groups. Which group I must chose to analyse (2 groups)? 

Group 0 ( System) 

Group 1 ( Protein)

Group 2 ( Protein-H) 

Group 3 ( C-alpha)

Group 4 ( Backbone) 

Group 5 ( MainChain) 

Group 6 ( MainChain+Cb) 

Group 7 ( MainChain+H) 

Group 8 ( SideChain) 

Group 9 ( SideChain-H) 

Group 10 ( Prot-Masses) 

Group 11 ( non-Protein) 

Group 12 ( Water) 

Group 13 ( SOL) 

Group 14 ( non-Water) 

Group 15 ( Ion)

Group 16 ( NA) 

Group 17 ( CL)

Group 18 ( Water_and_ions) 

Group 19 ( r_382) 

The position of mutation in this case in 382 (group 19). So, Is it fine to 19 and protein? 19 and protein-H? 19 and Backbone? 19 and MainChain/ MainChain+Cb/MainChain+H/SideChain/SideChain-H?

Thanks

More Faez Iqbal Khan's questions See All
Similar questions and discussions