Dear Amber users,
I am trying to analyse hydrogen
bonds using ptraj (AMBER8), I am not getting values
any suggestion is appreciated. Here is my ptraj
script file.
# H-bond analysis in cyclodextrine molecule
#
trajin b1_lg2_hb_con2_md_run2.crd 1 40 1
#-- Donors from beta cyclodextrine
donor mask :1-7.O2
donor mask :1-7.O3
donor mask :1-7.O4
donor mask :1-7.O5
donor mask :1-7.O6
#-- Acceptors from beta cyclodextrine
acceptor 4GA O2 H20
acceptor 4GA O3 H30
acceptor 4GA O6 H60
hbond distance 3.6 angle 160 print .05 series out
zzzz.out
Here I attached the out put file,
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Amber8 Module: ptraj
Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of .type)...
Read in residue labels...
4GA 4GA 4GA 4GA 4GA 4GA 4GA L2H WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...
Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...
Read in the JOIN info...
Read in the IROTAT info...
Scanning Box
Read in box information...
Successfully completed readParm.
PTRAJ: Processing input file...
Input is from file bcd-do-lig-acc.ptraj
PTRAJ: trajin b1_lg2_hb_con2_md_run2.crd 1 40 1
Checking coordinates: b1_lg2_hb_con2_md_run2.crd
PTRAJ: donor mask :1-7.O2
Mask [:1-7.O2] represents 7 atoms
PTRAJ: donor mask :1-7.O3
Mask [:1-7.O3] represents 7 atoms
PTRAJ: donor mask :1-7.O4
Mask [:1-7.O4] represents 7 atoms
PTRAJ: donor mask :1-7.O5
Mask [:1-7.O5] represents 7 atoms
PTRAJ: donor mask :1-7.O6
Mask [:1-7.O6] represents 7 atoms
PTRAJ: acceptor 4GA O2 H20
PTRAJ: acceptor 4GA O3 H30
PTRAJ: acceptor 4GA O6 H60
PTRAJ: hbond distance 3.6 angle 160 print .05 series
out zzzz.out
FYI: No output trajectory specified (trajout), none
will be saved.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 40 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (b1_lg2_hb_con2_md_run2.crd) is an AMBER
trajectory (with box info) with 40 sets
OUTPUT COORDINATE FILE
NULL entry
ACTIONS
1> HBOND saved to series out,
data will be sorted, intra-residue interactions
will NOT be included,
Distance cutoff is 3.60 angstroms, angle cutoff
is 160.00 degrees
Hydrogen bond information will be dumped for
occupancies > 0.05
Estimated memory usage for this hbond call:
0.02 MB
donors: 35 acceptors: 0
Processing AMBER trajectory file
b1_lg2_hb_con2_md_run2.crd
Set 1 ........................................
PTRAJ: Successfully read in 40 sets and processed 40
sets.
Dumping accumulated results (if any)
HBOND SUMMARY:
Data was saved to series out,
data was sorted, intra-residue interactions are
NOT included,
Distance cutoff is 3.60 angstroms, angle cutoff
is 160.00 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
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Received on Sun Jan 07 2007 - 06:07:07 PST
