CHARMM Development Project Forums CHARMM Community Script Archive hbonds.inp

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.

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 ô^A^@^@ CORD VELD
*** LEVEL -1 WARNING *** BOMLEV IS -3

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

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.

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.

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.

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.

HI,

I will do this by hand.

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

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

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.