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
Note in the help description of g_hbond:
"You need to specify two groups for analysis, which must be either identical or
non-overlapping. All hydrogen bonds between the two groups are analyzed."
So you need to construct your index groups appropriately. Likely none of the choices you have mentioned above will actually work, because they partially overlap.
Ultimately, the choice of group(s) for analysis depends on what is of interest in the system. Hydrogen bonds between one residue and the rest of the protein is a rather crude metric, and likely only a very few residues will ultimately be of interest. You can easily decide which to analyze by simply visualizing the trajectory, or by taking any existing information from the literature regarding biological function.
Thanks Justin.
I just want to see Hydrogen bond between one mutated residue(382) with rest of the protein. The results showing like a Bar Code (IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII).
Regards
FK
Then you need one index for the residue (which you have) and one that is the rest of the protein, except that residue (which you need to make).
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