[gmx-users] Re: g_hbond / hbmap.xpm file

[Thomas Schlesier]

 >atila petrosian wrote:
 >> > Dear Justin
 >> >
 >> > I confused.
 >> > number of donors in donor.xvg file is 203.  while, when use >g_hbond:
 >> > found 143 donors.
 >> >
 >I haven't taken a thorough look through the code (which is quite 
 >long), but it
 >looks like the number reported in donor.xvg considers all donor >groups,
 >including multiple H atoms on a donor (i.e., -NH2 has two donors), 
 >while the
 >number reported in the stdout corresponds to the fact that -NH2 is a 
 >donor
 >group.  Thus, the number in donor.xvg can be higher.
 >
 >Hopefully someone will correct me if I'm wrong.

I think Justin is right. g_hbond has the option -nomerge, where multiple 
H atoms are not merged to one donor. If you try your analysis again with 
-nomerge i think both donor-numbers would be the same.

greetings
thomas

 >
 >-Justin
 >
 >> > Select a group: 2
 >> > Selected 2: 'Protein_A'
 >> > Select a group: 3
 >> > Selected 3: 'Protein_B'
 >> > Checking for overlap in atoms between Protein_A and Protein_B
 >> > Calculating hydrogen bonds between Protein_A (1042 atoms) and 
 >Protein_B
 >> > (825 atoms)
 >> > Found 143 donors and 439 acceptors
 >> > Making hbmap structure...done.
 >> > Reading frame       0 time 19500.000
 >> > Will do grid-seach on 14x14x14 grid, rcut=0.35
 >> > Reading frame     120 time 19980.000
 >> > Found 40 different hydrogen bonds in trajectory
 >> > Found 69 different atom-pairs within hydrogen bonding distance
 >> > Merging hbonds with Acceptor and Donor swapped
 >> > 143/143
 >> > - Reduced number of hbonds from 40 to 40
 >> > - Reduced number of distances from 69 to 69
 >> > Average number of hbonds per timeframe 19.310 out of 31388.5 >possible
 >> >
 >> >
 >> >
 >-- ========