>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
>> >
>> >
>> >
>-- ========
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
