AMBER Archive (2009)

Subject: [AMBER] hbond_DNAtraj

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Mon Jun 01 2009 - 12:08:15 CDT

Dear Amber !

I am trying to find out the hbond details for the DNA ,

i have tried by seeing the archive
still i have the same problem

when i give the input file as
---------------------------------------------
trajin tmd_jun.mdcrd 0 10 1
trajout hbond_1.out

donor mask :1-40_at_O
acceptor mask :1-40_at_N :1-40_at_H

hbond includeself series h1 out hbond.dat distance 3.6 angle 120.0
---------------------------------------

when i run using this the log file is as follows.,
----------------------------------------------------------------
 $AMBERHOME/ptraj junction_tmd_source.prmtop < hbond.in

  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 9.0 integrated" (April 2006)
  -/- Executable is: "/home/programs/AMBERHOME/amber9/exe/ptraj"
  /-\
  \-/ Residue labels:

 DC5 DC DG DG DT DA DC DC DG DG3
 ...
 Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+
 ...
 Na+ Na+ Na+ Na+ Na+ Na+

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin tmd_jun.mdcrd 0 10 1
  Checking coordinates: tmd_jun.mdcrd

PTRAJ: trajout hbond_1.out

PTRAJ: donor mask :1-40_at_O
Mask [:1-40_at_O] represents 1260 atoms

PTRAJ: acceptor mask :1-40_at_N :1-40_at_H
Mask [:1-40_at_N] represents 1260 atoms
Mask [:1-40_at_H] represents 1260 atoms

PTRAJ: hbond includeself series h1 out hbond.dat distance 3.6 angle 120.0

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 10 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (tmd_jun.mdcrd) is an AMBER trajectory with 10 sets

OUTPUT COORDINATE FILE
  File (hbond_1.out) is an AMBER trajectory

ACTIONS
  1> HBOND saved to series h1, output to file hbond.dat,
      data will be sorted, intra-residue interactions will be included,
      Distance cutoff is 3.60 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information will be dumped for occupancies > 0.00
      Estimated memory usage for this hbond call: 218.04 MB
      donors: 1260 acceptors: 1260 frames: 10

Processing AMBER trajectory file tmd_jun.mdcrd

Set 1 ..........

PTRAJ: Successfully read in 10 sets and processed 10 sets.
       Dumping accumulated results (if any)

PTRAJ HBOND dumping summary to file hbond.dat

The hbond.data gives no information it is like as follows .

----------------------------------------------------------------------------
   HBOND SUMMARY:
      Data was saved to series h1, output to file hbond.dat,
      data was sorted, intra-residue interactions are included,
      Distance cutoff is 3.60 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information dumped for occupancies > 0.00

  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_at_atom atom# :res_at_atom atom# :res_at_atom %occupied distance angle lifetime maxocc
 ---------------- --------------------------------- -------------------------------------

please help me to solve this

thank you
regards
balaji

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