AMBER Archive (2009)

Subject: [AMBER] hbond_ptraj

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Mon May 25 2009 - 15:05:12 CDT

Dear Amber !

I am trying to calculate the hbond using ptraj

i am having some problem in getting the hbond.data

i saw the archive but i can not find out my mistake

I am doing it for DNA

the input file is
---------------------------------------------------------------
trajin tmd1.mdcrd 1 2
trajout hbondtry.out
donor mask :1-40_at_O
acceptor mask :1-40_at_N :1-40_at_H

hbond includeself distance 3.6 angle 120 out
intra_Hbond.out
-------------------------------------------------------------

the out put is
------------------------------------------------------------------------------
 1> HBOND
      data will be sorted, intra-residue interactions will be included,
      Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information will be dumped for occupancies > 0.00
      Estimated memory usage for this hbond call: 36.35 MB
      donors: 1260 acceptors: 1260

Processing AMBER trajectory file tmd1.mdcrd

Set 1 ..

PTRAJ: Successfully read in 2 sets and processed 2 sets.
       Dumping accumulated results (if any)

  HBOND SUMMARY:

      data was sorted, intra-residue interactions are included,
      Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information dumped for occupancies > 0.00

        DONOR ACCEPTORH ACCEPTOR
  atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied distance angle
 ---------------- --------------------------------- -------------------------------------

thanks
regards
balaji

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