AMBER: ptraj - hbond detailed analysis over time?

From: <>
Date: Thu, 26 May 2005 19:38:38 +0200 (MEST)

Dear developers and users,

I am using ptraj to analyse hbonds in an rna system. I get the mean hbond
occupancy, distance and angle for the donors and acceptors that I specify, as
well as the schematic time evolution. I would be interested in getting a
detailed time evolution printed to a separate file, which must somehow be
possible.. Here below are examples of an input I use and the respective output I
obtained. Thank you very much in advance!

Pascal Baillod


trajin ../traj.crd
acceptor mask :12.N3 :12.H3
donor mask :1.O6
hbond series hb time 0.75 distance 3.0 out 12Un3-1Go6.out


      Data was saved to series hb, output to file 12Un3-1Go6.out, time interval
is 0.75
      data was sorted, intra-residue interactions are NOT included,
      Distance cutoff is 3.00 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
  atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
angle lifetime maxocc
| 17 :1.O6 | 379 :12.H3 378 :12.N3 | 14.27 2.874 ( 0.08)
27.14 (13.24) 1.8 ( 2.4) 19 |--..-... |

Pascal Baillod (PhD student)
Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry
Room BCH 4121, Avenue Forel,
CH-1015 Lausanne
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu May 26 2005 - 18:53:00 PDT
Custom Search