Previous Thread
Next Thread
Print Thread
Page 3 of 6 1 2 3 4 5 6
Re: hbonds.inp
tong #263 04/18/06 06:24 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
lennart Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: hbonds.inp
lennart #264 04/18/06 08:21 PM
Joined: Jan 2006
Posts: 22
T
Forum Member
Offline
Forum Member
T
Joined: Jan 2006
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.

Re: hbonds.inp
tong #265 10/03/06 01:48 PM
Joined: Nov 2005
Posts: 51
N
nnn Offline
Forum Member
Offline
Forum Member
N
Joined: Nov 2005
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.

Re: hbonds.inp
nnn #266 10/03/06 03:06 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
lennart Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: hbonds.inp
lennart #267 10/04/06 05:55 AM
Joined: Nov 2005
Posts: 51
N
nnn Offline
Forum Member
Offline
Forum Member
N
Joined: Nov 2005
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.

Re: hbonds.inp
nnn #268 10/04/06 02:59 PM
Joined: Sep 2003
Posts: 8,505
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,505
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.


Rick Venable
computational chemist

Re: hbonds.inp
chuan #269 02/15/07 12:18 AM
Joined: Oct 2003
Posts: 39
Forum Member
Offline
Forum Member
Joined: Oct 2003
Posts: 39
HI,

I will do this by hand.

Last edited by zhangxd68; 02/15/07 05:22 AM.
Re: hbonds.inp [questions]
lennart #270 04/18/07 07:51 AM
Joined: Feb 2006
Posts: 4
B
Forum Member
Offline
Forum Member
B
Joined: Feb 2006
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

Re: hbonds.inp
lennart #271 05/09/08 09:13 AM
Joined: Jul 2004
Posts: 165
B
Forum Member
Offline
Forum Member
B
Joined: Jul 2004
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

Re: hbonds.inp
beginner #272 05/09/08 10:26 AM
Joined: Sep 2003
Posts: 4,796
Likes: 2
lennart Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Page 3 of 6 1 2 3 4 5 6

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.014s Queries: 34 (0.008s) Memory: 0.9940 MB (Peak: 1.1259 MB) Data Comp: Off Server Time: 2020-10-26 12:40:22 UTC
Valid HTML 5 and Valid CSS