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#263 - 04/18/06 02:24 PM Re: hbonds.inp [Re: tong]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Your CHARMM versions probably have been compiled with different settings for little_endian vs big_endian representation of binary data in unformatted files; for c32b1 on gnu/linux systems the default is big_endian with the intel and pgi compilers. It is easy to modify install.com to get the native format /little_endian/ to be used instead.
If your system uses the intel compiler this behavior can be changed at runtime without reinstallation; you can also convert the files you already have. Search the forums, or look at some recent posts on format of dcd files.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#264 - 04/18/06 04:21 PM Re: hbonds.inp [Re: lennart]
tong Offline
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Registered: 01/16/06
Posts: 22
Thank you very much Prof. Lennart.
I've checked the format dcd file, as you mentioned.
In my case c29b2 writes little_endian and c32b1 writes big_endian. After I changed dcd file (from c32) in big_endian format to little_endian (or little, c29, to big) but still can not analyse both trajectories together.

PROT 110 VAL HN - PROT 106 ILE O 5.00 250.00
PROT 111 ARG O - PROT 114 ALA HN 5.00 250.00
PROT 114 ALA HN - PROT 111 ARG O 5.00 250.00
***** ERROR ***** HEADERS DO NOT MATCH ^A^@^@ CORD VELD
*** LEVEL -1 WARNING *** BOMLEV IS -3

I have no idea how to deal with the header. Please help. Thank you.

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#265 - 10/03/06 09:48 AM Re: hbonds.inp [Re: tong]
nnn Offline
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Registered: 11/15/05
Posts: 51
Dear CHARMMERS,

From the hbond analysis output, I have seen some part of the output which looks like this:
Analysis of hydrogen bonds using cutoff distance= 2.80 and angle= 999.00
Total time= 600.0ps. Resolution= 5.00ps
Occupancy cutoff= 0.00 Lifetime cutoff= 0.0ps

I-atom J-atom <occupancy> <time> # events
---------------------------------------------------------------------------
PROT SER 2 O - PROT GLY 4 HN 0.62 11.9 31
PROT SER 2 O - PROT ILE 5 HN 0.83 29.1 17
PROT SER 2 O Summary: 1.44 20.5 48
PROT PRO 3 O - PROT ILE 5 HN 0.02 5.0 2
PROT GLY 4 HN - PROT SER 2 O 0.62 11.9 31
PROT GLY 4 O - PROT LYS 56 HN 1.00 600.0 1
PROT GLY 4 O - PROT THR 57 HN 1.00 600.0 1
PROT GLY 4 O Summary: 2.00 600.0 2

If I would like to the find % occupation of hbond , for example, % hbond occupation of the O-Ser2 and other residues, how can I obtain it?

I am not sure if I can use "1.44*100" because it's higher than 100%. If I think that 100% means this kind of hbond occurs entire the simulation time, how can I calculate the % hbond occupation? Any advice would be appreciated. Thank you.

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#266 - 10/03/06 11:06 AM Re: hbonds.inp [Re: nnn]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
The carbonyl of Ser 2 apparently hydrogen bonds to the amides of Gly4 and Ile5, partly at the same time. 1.44*100 is correct if you want to express this total occpancy as a percentage.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#267 - 10/04/06 01:55 AM Re: hbonds.inp [Re: lennart]
nnn Offline
Forum Member

Registered: 11/15/05
Posts: 51
Thank you Prof. Lennart. From your reply, it means that % hbond occupation can higher than 100%, is my understanding correct? First I though that the highest value could be 100% but I am not sure.

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#268 - 10/04/06 10:59 AM Re: hbonds.inp [Re: nnn]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
The maximum fractional occupancy is 1.0 when there is a 1:1 correspondence between donor and acceptor, but a good H-bond acceptor can have 2 donors, and the fractional occupancy can exceed 1.0 in that case.
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Rick Venable
computational chemist


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#269 - 02/14/07 07:18 PM Re: hbonds.inp [Re: chuan]
zhangxd68 Offline
Forum Member

Registered: 10/31/03
Posts: 39
HI,

I will do this by hand.


Edited by zhangxd68 (02/15/07 12:22 AM)

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#270 - 04/18/07 03:51 AM Re: hbonds.inp [questions] [Re: lennart]
bryanleech Offline
Forum Member

Registered: 02/15/06
Posts: 4
Hi,

1) When i was doing analysis for a trajectory for a 20ns simulation with 2000 frames with:
"coor hbond verbose sele monitor end sele .not. monitor end firstu 20 nunits 1 begin 10000 skip 10000"

the following was observed in the output:
Analysis of hydrogen bonds using cutoff distance= 2.40 and angle= 999.00
Total time= 977.8ps. Resolution= 0.49ps
Occupancy cutoff= 0.00 Lifetime cutoff= 0.0ps

>> why only 977.8 ps?

2) the spec "skip" and "nskip" for the traj-spec is same?

regards,
Bryan

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#271 - 05/09/08 05:13 AM Re: hbonds.inp [Re: lennart]
beginner Offline
Forum Member

Registered: 07/19/04
Posts: 165
Dear Prof. Nilsson,
I would like to analyze the hydrogen bond between lipid and peptide to compare with the literature. The criteria that they use is the hydrogen bond said to exist if donor -acceptor distance is < 2.5 angstrom and the donor-hydrogen..acceptor hydrogen bond form angle > 145 degree. to set that, I would say cuthb 2.5, but to set the angle I could not simply say cutha 145, correct? how could I reach that angle? thank you

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#272 - 05/09/08 06:26 AM Re: hbonds.inp [Re: beginner]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Why not? From corman.doc:
"[hydrogen bond exists if ] the angle formed by D-H..A is greater than this CUTAngle (in degrees, 180 is a linear H-bond)".

Note that adding the angular criterion makes almost no difference in practice.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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