Dear Amber users,
I am trying to analyse hydrogen
bonds using ptraj (AMBER8). It shows that donors: 35
and acceptors: 0. Is it wrong in defing acceptors?
Here is input 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
Can any one coorect me where i did wrong?
Thanks in advance
nagaraju
here is out put file
###############################################
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
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Received on Sun Jan 07 2007 - 06:07:18 PST
