Justin A. Lemkul skrev 2010-11-10 14.57:
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
Not sure, but I think you're right. Try g_hbond -nomerge
Erik
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
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
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