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
--
========================================
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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