Dear Users
I want to do hydrogen bond analysis for protein-ligand docked complex...my
input file is as fellows:
trajin prod_1-8.binpos
#trajout trj.peptide nobox
#Center the geometry of the residues listed to the origin
#center :0-210
#image origin center
# specify the electron pair DONOR
donor mask :LEU198.O
donor mask :LEU198.N
donor mask :ILE196.O
# specify the ACCEPTOR(s)
acceptor mask :196.H :374.N1
acceptor mask :210.HH12 :374.O1
acceptor mask :210.HH11 :374.O2
acceptor mask :98.H :374.O4
#hbond command options
hbond series hbond out hbond.out time 1.0 distance 3.5 angle 120.0
#hbond distance 3.5 angle 120.0 donor LEU198.O donor LEU198.N donor
ILE196.Oacceptor 196.H
:374.N1 acceptor 210.HH12 :374.O1 acceptor 210.HH11 :374.O2 acceptor
98.H:374.O4neighbor 2 series hbond
#-- series hbt is just a placeholder to ensure we get the full analysis. If
you don't
#have the word series you don't get a full analysis.
hbond print .05 series hbt
*Output produced is :*
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 12.0 integrated" (4/2012)
-/- Executable is: "ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
MET GLY SER SER GLU ASP GLN ALA TYR ARG
LEU LEU ASN ASP TYR ALA ASN GLY PHE MET
VAL SER GLN VAL LEU PHE ALA ALA CYS GLU
LEU GLY VAL PHE ASP LEU LEU ALA GLU ALA
PRO GLY PRO LEU ASP VAL ALA ALA VAL ALA
ALA GLY VAL ARG ALA SER ALA HIE GLY THR
GLU LEU LEU LEU ASP ILE CYS VAL SER LEU
LYS LEU LEU LYS VAL GLU THR ARG GLY GLY
LYS ALA PHE TYR ARG ASN THR GLU LEU SER
SER ASP TYR LEU THR THR VAL SER PRO THR
SER GLN CYS SER MET LEU LYS TYR MET GLY
ARG THR SER TYR ARG CYS TRP GLY HIE LEU
ALA ASP ALA VAL ARG GLU GLY ARG ASN GLN
TYR LEU GLU THR PHE GLY VAL PRO ALA GLU
GLU LEU PHE THR ALA ILE TYR ARG SER GLU
GLY GLU ARG LEU GLN PHE MET GLN ALA LEU
GLN GLU VAL TRP SER VAL ASN GLY ARG SER
VAL LEU THR ALA PHE ASP LEU SER VAL PHE
PRO LEU MET CYS ASP LEU GLY GLY THR TRP
ILE LYS LEU GLU THR ILE ILE LEU SER LYS
LEU SER GLN GLY GLN LYS THR LYS HIE ARG
VAL PHE SER LEU ILE GLY GLY ALA GLY ALA
LEU ALA LYS GLU CYS MET SER LEU TYR PRO
GLY CYS LYS ILE THR VAL PHE ASP ILE PRO
GLU VAL VAL TRP THR ALA LYS GLN HIE PHE
SER PHE GLN GLU GLU GLU GLN ILE ASP PHE
GLN GLU GLY ASP PHE PHE LYS ASP PRO LEU
PRO GLU ALA ASP LEU TYR ILE LEU ALA ARG
VAL LEU HID ASP TRP ALA ASP GLY LYS CYS
SER HIE LEU LEU GLU ARG ILE TYR HID THR
CYS LYS PRO GLY GLY GLY ILE LEU VAL ILE
GLU SER LEU LEU ASP GLU ASP ARG ARG GLY
PRO LEU LEU THR GLN LEU TYR SER LEU ASN
MET LEU VAL GLN THR GLU GLY GLN GLU ARG
THR PRO THR HIE TYR HIE MET LEU LEU SER
SER ALA GLY PHE ARG ASP PHE GLN PHE LYS
LYS THR GLY ALA ILE TYR ASP ALA ILE LEU
ALA ARG LYS UNK WAT WAT WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT WAT
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin prod_1-8.binpos
Checking coordinates: prod_1-8.binpos
PTRAJ: donor mask :LEU198.O
Mask [:LEU198.O] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:LEU198.O), ignoring...
PTRAJ: donor mask :LEU198.N
Mask [:LEU198.N] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:LEU198.N), ignoring...
PTRAJ: donor mask :ILE196.O
Mask [:ILE196.O] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:ILE196.O), ignoring...
PTRAJ: acceptor mask :196.H :374.N1
Mask [:196.H] represents 1 atoms
Mask [:374.N1] represents 1 atoms
PTRAJ: acceptor mask :210.HH12 :374.O1
Mask [:210.HH12] represents 1 atoms
Mask [:374.O1] represents 1 atoms
PTRAJ: acceptor mask :210.HH11 :374.O2
Mask [:210.HH11] represents 1 atoms
Mask [:374.O2] represents 1 atoms
PTRAJ: acceptor mask :98.H :374.O4
Mask [:98.H] represents 1 atoms
Mask [:374.O4] represents 1 atoms
PTRAJ: hbond series hbond out hbond.out time 1.0 distance 3.5 angle 120.0
PTRAJ: hbond print .05 series hbt
[No output trajectory specified (trajout)]
prod_1-8.binpos: 16004 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 16004 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (prod_1-8.binpos) is a BINPOS file with 16004 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> HBOND saved to series hbond, output to file hbond.out, inter-solvent
hbonds will not be included,
data will be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 0.73 MB
donors: 0 acceptors: 4 frames: 16004
2> HBOND saved to series hbt, inter-solvent hbonds will not be included,
data will be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.05
Estimated memory usage for this hbond call: 0.73 MB
donors: 0 acceptors: 4 frames: 16004
Processing BINPOS file prod_1-8.binpos
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 16004 sets and processed 16004 sets.
Dumping accumulated results (if any)
PTRAJ HBOND dumping summary to file hbond.out
HBOND SUMMARY:
Data was saved to series hbt,
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 3.00 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
---------------- ---------------------------------
-------------------------------------
*NO values/percentages generated..*........
Is my input file correct???
I am sure it is very simple but i am not able to put my figure on
it........Kindly help me out.
Regards
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
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Received on Wed Sep 18 2013 - 03:00:03 PDT
