Dear all,
during my hbond analysis - of one my residuum (ANS) and 10 closest waters
I obtained
strange output from the point of view of water acceptors. Instead of "O"
it writes
"H1" which is nonsence and moreover it is at variance with my input
information.
So or I have some error in my input or there is some problem in hbond
routine.
If anyone see any mistake in my input please let me know.
Best wishes,
Marek
-------------RELEVANT PART OF PTRAJ INPUT FILE
-------------RELEVANT PART OF PTRAJ INPUT FILE
-------------RELEVANT PART OF PTRAJ INPUT FILE
trajin prod_BASE_NAME_REIMAGED.mdcrd 1 400 1
donor ANS O1
donor ANS O2
donor ANS O3
acceptor ANS N H7
acceptor WAT O H1
acceptor WAT O H2
donor WAT O
strip :Na+
solvent byres :WAT
closestwater 10 :ANS first noimage
hbond distance 3.5 angle 120.0 print .05 series hbt
-------------RELEVANT PART OF PTRAJ OUTPUT FILE
-------------RELEVANT PART OF PTRAJ OUTPUT FILE
-------------RELEVANT PART OF PTRAJ OUTPUT FILE
HBOND SUMMARY:
Data was saved to series hbt,
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information dumped for occupancies > 0.05
Dumping schematic of time series after each h-bond, key follows:
| . - o x * . |
0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy
DONOR ACCEPTORH ACCEPTOR
atom# :res.atom atom# :res.atom atom# :res.atom %occupied
distance angle lifetime maxocc
| 3498 :190.O3 | 3536 :193.H2 3535 :193.H1 | 10.50 3.045 (
0.14) 39.68 (11.60) 1.1 ( 0.3) 2 |-... .. ... .-. --. -..
--.- . .--- . |
| 3498 :190.O3 | 3539 :194.H2 3538 :194.H1 | 10.25 3.143 (
0.13) 37.05 ( 8.91) 1.2 ( 0.4) 2 |--. .. -.----- .--
.-. --. .- . |
| 3498 :190.O3 | 3542 :195.H2 3541 :195.H1 | 9.50 3.180 (
0.12) 36.51 (12.45) 1.1 ( 0.4) 3 |.. ..-- -.-. .-. ...
...-. .. -.-. -|
| 3498 :190.O3 | 3533 :192.H2 3532 :192.H1 | 8.25 3.068 (
0.14) 35.76 (11.38) 1.2 ( 0.6) 4 |.-. - o.. o . ...o ..-
. . . . |
| 3498 :190.O3 | 3530 :191.H2 3529 :191.H1 | 7.50 3.059 (
0.15) 37.90 ( 9.94) 1.1 ( 0.3) 2 |-.. .. - - . .. . .. ..
-- . - ..- |
| 3498 :190.O3 | 3545 :196.H2 3544 :196.H1 | 6.50 3.186 (
0.14) 37.62 (12.36) 1.1 ( 0.3) 2 | . .. - ..- .-...
- . - .. . |
| 3498 :190.O3 | 3548 :197.H2 3547 :197.H1 | 6.25 3.201 (
0.12) 40.53 (10.54) 1.2 ( 0.4) 2 | .- . ...-- . . ...
.- . .- |
| 3498 :190.O3 | 3551 :198.H2 3550 :198.H1 | 5.00 3.272 (
0.12) 38.27 (10.45) 1.0 ( 0.0) 1 | . . . ... .......
. . .. -. |
---------------- ---------------------------------
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Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Fri May 06 2011 - 13:30:02 PDT
