AMBER Archive (2007)

Subject: AMBER: H-acceptors problem in ptraj

From: nag raj (nagaraju_chem_at_yahoo.co.in)
Date: Wed Jan 03 2007 - 23:20:09 CST

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_at_O2
donor mask :1-7_at_O3
donor mask :1-7_at_O4
donor mask :1-7_at_O5
donor mask :1-7_at_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_at_O2
Mask [:1-7_at_O2] represents 7 atoms

PTRAJ: donor mask :1-7_at_O3
Mask [:1-7_at_O3] represents 7 atoms

PTRAJ: donor mask :1-7_at_O4
Mask [:1-7_at_O4] represents 7 atoms

PTRAJ: donor mask :1-7_at_O5
Mask [:1-7_at_O5] represents 7 atoms

PTRAJ: donor mask :1-7_at_O6
Mask [:1-7_at_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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