Hi
I am trying to perform hydrogen bond analysis on a trajectory using amber9.
The problem is that command input requires the ACCEPTORH to be specified
with the acceptor atom
and when I looked into the PDB file the potential acceptor atoms of ASP and
GLU, among others, didn't have these ACCEPTORH connected to them. So I
tried to put in atoms that could be there but the hbond command in pTraj
rejects these atoms and there is no output. However, there is only one
proper PAIR of the acceptor atoms (a THR -OH group) that is accepted by
ptraj as it has ONE-to-ONE corresponence.. rest are ignored.
THIS is how the output (partial ) appears on the screen:---
PTRAJ: acceptor :MAN .OM* OM*H
PTRAJ: acceptor mask .O .H
Mask [.O] represents 237 atoms
Mask [.H] represents 225 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks .O and .H which contain 237 and 225
atoms respectively. Ignoring...
PTRAJ: acceptor mask .OD1
WARNING in ptraj, acceptor: Error in mask specification. Ignoring...
PTRAJ: acceptor mask .OD2
WARNING in ptraj, acceptor: Error in mask specification. Ignoring...
PTRAJ: acceptor mask .OG1 .HG1
Mask [.OG1] represents 19 atoms
Mask [.HG1] represents 19 atoms
PTRAJ: acceptor mask .OE1 .HE1
Mask [.OE1] represents 12 atoms
Mask [.HE1] represents 30 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks .OE1 and .HE1 which contain 12 and 30
atoms respectively. Ignoring...
PTRAJ: acceptor mask .OE2 .HE2
Mask [.OE2] represents 7 atoms
Mask [.HE2] represents 38 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks .OE2 and .HE2 which contain 7 and 38
atoms respectively. Ignoring...
PTRAJ: acceptor mask .OH .HO
Mask [.OH] represents 7 atoms
Mask [.HO] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No hydrogen atom was selected (.HO), ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks .OH and .HO which contain 7 and 0
atoms respectively. Ignoring...
PTRAJ: acceptor mask .OG .HG
Mask [.OG] represents 31 atoms
Mask [.HG] represents 49 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks .OG and .HG which contain 31 and 49
atoms respectively. Ignoring...
ACTIONS
1> STRIP: 18762 atoms will be removed from trajectory: :239-6492
7> CENTER to box center via center of geometry, atom selection follows
* (All atoms are selected)
7> HBOND saved to series hbond1.out,
data will be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.60 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 65.80 MB
donors: 302 acceptors: 19 frames: 1000
HBOND SUMMARY:
Data was saved to series hbond1.out,
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 3.60 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information dumped for occupancies > 0.00
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
| 770 :51.ND1 | 2932 :194.HG1 2931 :194.OG1 | 67.30 3.019 (
0.19) 35.47 (13.28) 4.3 ( 5.0) 31 |*xxxx*xxxx-oxx**-xxo|
| 3150 :209.N | 157 :11.HG1 156 :11.OG1 | 13.80
3.352 ( 0.16) 49.82 ( 7.83) 1.4 ( 0.8) 4 |
---.....-----|
| 223 :16.N | 220 :15.HG1 219 :15.OG1 | 10.20
3.479 ( 0.08) 50.61 ( 6.23) 1.3 ( 0.5) 3 |..--... . .. .-
..|
| 1582 :104.ND2 | 2402 :157.HG1 2401 :157.OG1 | 9.90 3.310 ( 0.19)
53.36 ( 5.55) 1.2 ( 0.6) 5 | .-.--- ... .. ..|
| 160 :12.N | 157 :11.HG1 156 :11.OG1 | 3.40
3.472 ( 0.10) 51.43 ( 6.02) 1.2 ( 0.5) 3 | ..
.. . |
| 3128 :207.N | 157 :11.HG1 156 :11.OG1 | 1.30
3.516 ( 0.09) 52.78 ( 6.74) 1.1 ( 0.3) 2 | .
. |
| 1940 :127.ND1 | 1716 :112.HG1 1715 :112.OG1 | 0.90 2.907 ( 0.14)
38.08 (12.68) 2.2 ( 0.8) 3 |. |
| 2068 :135.N | 2281 :148.HG1 2280 :148.OG1 | 0.80 3.465 (
0.14) 53.18 ( 4.75) 1.0 ( 0.0) 1 | .. |
| 1843 :121.N | 1840 :120.HG1 1839 :120.OG1 | 0.80 3.402 (
0.15) 50.74 ( 6.49) 1.0 ( 0.0) 1 | |
| 773 :51.NE2 | 2932 :194.HG1 2931 :194.OG1 | 0.20 3.247 (
0.17) 51.20 ( 5.59) 1.0 ( 0.0) 1 | |
| 3399 :227.N | 3396 :226.HG1 3395 :226.OG1 | 0.10 3.472 (
0.00) 58.90 ( 0.00) 1.0 ( 0.0) 1 | |
| 3265 :216.ND2 | 36 :3.HG1 35 :3.OG1 | 0.10
3.500 ( 0.00) 16.87 ( 0.00) 1.0 ( 0.0) 1
| |
| 1573 :104.N | 1570 :103.HG1 1569 :103.OG1 | 0.10 3.542 (
0.00) 58.48 ( 0.00) 1.0 ( 0.0) 1 | |
---------------- ---------------------------------
-------------------------------------
So i wanted to ask that how can I get data about ASP, GLU, etc where the
acceptorH atoms are absent in the PDB file and trajectory as well probably
due to pH 7 implicitly ...
And i want to know the same about the OH groups present in MANNOSE , as they
also lack proper acceptor atoms in the PDB and
trajectory...
I have tried AMBER9 manual but it doesn't mention this problem or its
solution...
Please let me know what can be done..
Thanks to all...
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Received on Wed Apr 18 2007 - 06:07:13 PDT
