Hello,

I also have questions of the output od hydrogen bond analysis even I've read the above posted but it's still unclear to me.

In protein-proetin output section, I have:

Analysis of hydrogen bonds using cutoff distance= 2.40 and angle= 999.00
I-atom J-atom r(H-A) [A] D-H..A [deg]
--------------------------------------------------------------------
PROT GLY 4 O - PROT LYS 56 HN 1.90 168.7
PROT GLY 4 O - PROT THR 57 HN 1.86 157.8
PROT TRP 6 HN - PROT THR 57 O 1.88 169.8
PROT TRP 6 O - PROT HSD 59 HN 1.99 163.5
PROT GLN 7 HN - PROT VAL 22 O 1.79 167.7
PROT GLN 7 O - PROT VAL 22 HN 1.89 170.1
PROT LEU 8 HN - PROT HSD 59 O 1.77 175.0
PROT THR 11 HN - PROT ILE 18 O 1.86 165.5
PROT THR 11 O - PROT ILE 18 HN 1.91 159.1

and the lifetime section is:

I-atom J-atom (Bridge) Lifetime Endtime
PROT 2 SER HN - PROT 2 SER O 5.00 10.00
PROT 2 SER O - PROT 2 SER HN 5.00 10.00
PROT 5 ILE O - PROT 24 VAL HN 5.00 10.00
PROT 17 VAL HN - PROT 17 VAL O 5.00 10.00
PROT 17 VAL O - PROT 17 VAL HN 5.00 10.00
PROT 24 VAL HN - PROT 5 ILE O 5.00 10.00
PROT 41 GLU O - PROT 45 PHE HN 5.00 10.00
PROT 45 PHE HN - PROT 41 GLU O 5.00 10.00

My questions are:
1. For lifetime section, Does the first line mean that the bridge between HN of SER2 and O of the same residue occurs within 5ps and it will be broken after 10 ps? I just want to make sure whether I'm correctly understand.

2. Why the lines of the first section (protein-protein output section in this case) are not match with the lines of the lifetime section? For example,

If the protein-protein section starts with

PROT GLY 4 O - PROT LYS 56 HN 1.90 168.7
PROT GLY 4 O - PROT THR 57 HN 1.86 157.8
PROT TRP 6 HN - PROT THR 57 O 1.88 169.8

The lifetime section should also start with:

I-atom J-atom (Bridge) Lifetime Endtime

PROT GLY 4 O - PROT LYS 56 HN ... ....
PROT GLY 4 O - PROT THR 57 HN ... ....
PROT TRP 6 HN - PROT THR 57 O ... ....

Thanks in advance.