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#253 - 04/23/05 02:41 PM Re: hbonds.inp [Re: Leonardo]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Your interpretation of the lifetime and endtime columns is correct. I do not think that you have to worry about the angular dependence - in practice it works very well with just a distance dependent cutoff on the H-Acceptor distance (see J. Am. Chem. Soc., 1992. 114: p. 4028-4035). It may be that more distorted hydrogen bonds do actually occur in implicit solvent simulations (I have not looked at this, so it is just a speculation).
Note that with a 100 step resolution you may underestimate the hydrogen bond lifetimes; we normally use a resolution of 1-5 ps.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#254 - 06/01/05 05:48 AM Re: hbonds.inp [Re: lennart]
chuan Offline
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Registered: 05/17/04
Posts: 222
In determining prot-water-ligand bridges, i've specified 'tip3 .and. resi 136' instead of 'TIP3' to make it more specific. There is no error in the output but i cant be sure it is correct. Can someone confirm? The command are as followed:
coor hbond verbose cuthb @CUTHB cutha @CUTHA select ONE end select TWO end-
bridge tip3 .and. resi 136 firstu 51 nunit @N skip @SKIP
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#255 - 06/01/05 06:36 AM Re: hbonds.inp [Re: chuan]
lennart Online   content

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Registered: 09/25/03
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Loc: ~ 59N, 15E
Incorrect, but you can achieve this effect by renaming tip3 136:
rename resn t136 select atom wat 136 * end
coor hbond ... bridge t136 ....

It is typically not necessary to define a cutoff for the angle.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#256 - 01/25/06 10:26 AM Re: hbonds.inp [Re: lennart]
PKo Offline
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Registered: 01/12/04
Posts: 91
hi,

i would like to know how to interpret the results of lifetime and endtime. as i read the post on hbonds, it is still not clear with the output i have.

######################################################

I-atom J-atom (Bridge) Lifetime Endtime
LEC 201 ASP OD1 - MIC 13 BOG HO4 60.00 70.00
LEC 201 ASP OD2 - MIC 13 BOG HO3 140.00 150.00
LEC 201 ASP OD2 - MIC 13 BOG HO3 120.00 280.00
LEC 201 ASP OD1 - MIC 13 BOG HO4 230.00 310.00
LEC 173 LEU O - MIC 20 BOG HO3 70.00 410.00
LEC 195 ASP OD2 - MIC 8 BOG HO4 90.00 410.00
LEC 195 ASP OD2 - MIC 8 BOG HO4 100.00 520.00
LEC 145 LYS HZ2 - MIC 16 BOG O4 90.00 740.00
LEC 195 ASP OD1 - MIC 8 BOG HO4 150.00 770.00
LEC 108 GLU OE2 - MIC 16 BOG HO2 90.00 800.00
LEC 129 ASP OD1 - MIC 16 BOG HO4 150.00 800.00
LEC 145 LYS HZ2 - MIC 16 BOG O2 190.00 800.00

I-atom J-atom (Bridge) Lifetime Endtime
LEC 100 TYR O - MIC 16 BOG O4 WAT1 7106 250.00 260.00
LEC 174 THR O - MIC 20 BOG O6 WAT1 6496 60.00 470.00
LEC 192 THR OG1 - MIC 8 BOG HO6 WAT1 5614 60.00 520.00

#########################################################

as seen in the second and third row the protein and lipid atoms are the same except their two different lifetime and endtimes. which one should i consider in this case.

in general:--

the endtime --- is it the actual residence time b/n those atoms?

the lifetime --- is it the duration of active hbond ?

thank you

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#257 - 01/25/06 10:57 AM Re: hbonds.inp [Re: PKo]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
In this section of the verbose-mode output the endtime is the timepoint at which this particular instance of the bond between these two atoms was broken. The lifetime is the duration of this particular instance of the hydrogen bond or bridge.
Thus the information in your second and third rows means that there was a hydrogen bond between these atoms in the two intervals (10,150) and (160,280).

You are probably better off looking at the more compact summary information at the end of the output.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#258 - 04/17/06 09:10 PM Re: hbonds.inp [Re: lennart]
tong Offline
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Registered: 01/16/06
Posts: 22
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.

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#259 - 04/18/06 08:29 AM Re: hbonds.inp [Re: tong]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
1/ Yes, your understanding is correct.
2/ You are apparently looking at two different COOR HBOND outputs. The one you call protein-protein is from a static analysis of a single coordinate set; a similar output, but with hydrogen bond lifetime data, is printed from the analysis of a trajectory. Your other output, which you call lifetime section, is simply a chronological record of all hydrogen bond forming/breaking events in the trajectory, as such it is time-ordered; it is usually not necessary to look at this output. The summary information, giving the average occupancies and lifetimes is more informative and easier to grasp.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#260 - 04/18/06 11:09 AM Re: hbonds.inp [Re: lennart]
tong Offline
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Registered: 01/16/06
Posts: 22
Hello,

Thank you Prof. Lennart. However I still have questions.

I've looked at the summary section and I've found something like this:

I-atom J-atom <occupancy> <time> # events
---------------------------------------------------------------------------
PROT SER 2 HN - PROT SER 2 O 0.44 18.3 6
PROT SER 2 O - PROT SER 2 HN 0.44 18.3 6
PROT SER 2 O - PROT GLY 4 HN 0.06 7.5 2
PROT SER 2 O - PROT ILE 5 HN 0.28 7.8 9
PROT SER 2 O Summary: 0.78 11.2 17
PROT GLY 4 HN - PROT SER 2 O 0.06 7.5 2
PROT GLY 4 O - PROT LYS 56 HN 1.00 250.0 1
PROT GLY 4 O - PROT THR 57 HN 0.98 122.5 2
PROT GLY 4 O Summary: 1.98 186.2 3
PROT ILE 5 HN - PROT SER 2 O 0.28 7.8 9
PROT ILE 5 O - PROT VAL 24 HN 0.08 5.0 4
PROT TRP 6 HN - PROT TRP 6 O 0.10 5.0 5
PROT TRP 6 HN - PROT THR 57 O 1.00 250.0 1
PROT TRP 6 HN Summary: 1.10 127.5 6


My questions are:

1. what's the meaning of time and events? Are the time and event refer to the duration of h-bond (ps) and a numbers of time that we can find this h-bond, respectively? And what's the maximum value of "summary of occupancy" per residue?

2. In the last section of this summary, I've found:

OVERALL
Average number (over ISEL!)= 0.6
<lifetime>= 83.52ps
Total number/frame= 175.3

Is the "lifetime" refer to the total lifetime or what?

Thanks in advance.

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#261 - 04/18/06 11:21 AM Re: hbonds.inp [Re: tong]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
<...> means average. The symbol # means "number". So "<time>" means "average [life]time" (in ps) and "# events" means "number [of] events", ie how many times this hydrogen bond was formed. I do not know exactly what the maximum number of the occupancy would be since it depends on how many simultaneous hydrogen bonds that particular atom can form; the summary is not per residue. The final numbers are the averages over all selected donors/acceptors over the whole trajectory. Check corman.doc.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#262 - 04/18/06 12:00 PM Re: hbonds.inp [Re: lennart]
tong Offline
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Registered: 01/16/06
Posts: 22
Thank you to Prof. Lennart for your clarification.

For my question below, I'm not sure whether I should post it here or should be in another section.

I just have problem on h-bond analysis when reading more than 1 trajectory. For example, I used charmm 29b2 to simulate the first trajectory and used c32b1 for the other trajectories (because we just have c32b1).

I can not use neither c29b2 nor c32b1 to analyse all trajectories produced by both c29b2 and c32b1.The header produced by c29b2 and c32b1 does not match each other. However, if I use c29b2 to analyse only trajectory produced by c29b2 or vice versa for c32b1, it works well. I'd like to know that are there any possiblities to read trajectories produced by different versions of charmm wihtout any configtion.

Thanks in advance.

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