[gmx-users] -don (g-hbond)

[Justin A. Lemkul]

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.

-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
>  
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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