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

[Erik Marklund]

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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/