Dear Users
I want to calculate H-bond analysis of protein-ligand complex, after
20ns of MD simulation. I have specified the position of H-bond in the
input files, yet the output display "WARNING in ptraj(), hbond: No
list of hbond donors/acceptors has been".
Below is the output files
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 10.0 integrated" (2/15/2008)
-/- Executable is: "ptraj"
/-\
\-/ Residue labels:
MET SER GLU GLY PRO LYS LYS ALA GLY VAL
LEU GLY SER PRO ILE ALA HIE SER ARG SER
PRO GLN LEU HIE LEU ALA ALA TYR ARG ALA
LEU GLY LEU HIE ASP TRP THR TYR GLU ARG
ILE GLU CYS GLY ALA ALA GLU LEU PRO VAL
VAL VAL GLY GLY PHE GLY PRO GLU TRP VAL
GLY VAL SER VAL THR MET PRO GLY LYS PHE
ALA ALA LEU ARG PHE ALA ASP GLU ARG THR
ALA ARG ALA ASP LEU VAL GLY SER ALA ASN
THR LEU VAL ARG THR PRO HIE GLY TRP ARG
ALA ASP ASN THR ASP ILE ASP GLY VAL ALA
GLY ALA LEU GLY ALA ALA ALA GLY HIE ALA
LEU VAL LEU GLY SER GLY GLY THR ALA PRO
ALA ALA VAL VAL GLY LEU ALA GLU LEU GLY
VAL THR ASP ILE THR VAL VAL ALA ARG ASN
SER ASP LYS ALA ALA ARG LEU VAL ASP LEU
GLY THR ARG VAL GLY VAL ALA THR ARG PHE
CYS ALA PHE ASP SER GLY GLY LEU ALA ASP
ALA VAL ALA ALA ALA GLU VAL LEU VAL SER
THR ILE PRO ALA GLU VAL ALA ALA GLY TYR
ALA GLY THR LEU ALA ALA ILE PRO VAL LEU
LEU ASP ALA ILE TYR ASP PRO TRP PRO THR
PRO LEU ALA ALA ALA VAL GLY SER ALA GLY
GLY ARG VAL ILE SER GLY LEU GLN MET LEU
LEU HIE GLN ALA PHE ALA GLN VAL GLU GLN
PHE THR GLY LEU PRO ALA PRO ARG GLU ALA
MET THR CYS ALA LEU ALA ALA LEU ASP NK0
Na+ Na+ Na+ Na+ Na+ WAT WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
Setting box to be an exact truncated octahedron, angle is 109.471221
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin prod.mdcrd
Checking coordinates: prod.mdcrd
PTRAJ: hbond all out hbond.agr :19, 88, 128.C,O,N,H time 20.00
WARNING in ptraj(), hbond: No list of hbond donors/acceptors has been
specified. Ignoring command...
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 2000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (prod.mdcrd) is an AMBER trajectory (with box info) with 2000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
NO ACTIONS WERE SPECIFIED
Processing AMBER trajectory file prod.mdcrd
Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500 .................................................
Set 550 .................................................
Set 600 .................................................
Set 650 .................................................
Set 700 .................................................
Set 750 .................................................
Set 800 .................................................
Set 850 .................................................
Set 900 .................................................
Set 950 .................................................
Set 1000 .................................................
Set 1050 .................................................
Set 1100 .................................................
Set 1150 .................................................
Set 1200 .................................................
Set 1250 .................................................
Set 1300 .................................................
Set 1350 .................................................
Set 1400 .................................................
Set 1450 .................................................
Set 1500 .................................................
Set 1550 .................................................
Set 1600 .................................................
Set 1650 .................................................
Set 1700 .................................................
Set 1750 .................................................
Set 1800 .................................................
Set 1850 .................................................
Set 1900 .................................................
Set 1950 .................................................
Set 2000
PTRAJ: Successfully read in 2000 sets and processed 2000 sets.
Dumping accumulated results (if any)
--
Warm regards
Mustafa Alhaji Isa
Department of Microbiology,
Faculty of Sciences
University of Maiduguri,
Borno State,
Nigeria
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Received on Wed Nov 08 2017 - 04:30:01 PST
