Hi all,
This question my seem somewhat trivial, however...here goes. From what I gather, the latest version of the ptraj H-bond analysis tool outputs a string of 50 characters, each indicating the H-bond occupancy for each 50th of the trajectory. For my job, I use the basic skeleton of the script used in the respective ptraj tutorial, editing donor and acceptors specific for my system. I get no errors throughout the ptraj run and the job completes fine. I checked the mdcrd file which contains 1000 frames, as expected and I strip waters just before the hbond command (to avoid prmtop inconsistencies).
The problem I have is that in my output I'm only getting 48 symbols....indicating each symbol only accounts for 1/48th of the simulation. Has this been seen before and is there any explanation for this?
Many Thanx,
Maura
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 10 2011 - 19:30:03 PDT
