AMBER Archive (2009)

Subject: [AMBER] ptraj_hbond_problem

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Thu Jun 04 2009 - 17:08:24 CDT

Dear AMBER !

I have searched the archive and get cleared and gave the input as
-----------------------------------------------------------
trajin tmd1.mdcrd 1 2
trajout origihbondtry.out

donor mask :1-40_at_O

acceptor mask :1-40_at_N : 1-40_at_H
hbond series h1 out hbond.dat includeself distance 3.6 angle 160 out
-------------------------------------------------------------------------------
I am getting problem in finding out the hbond in DNA trajectory

this time i am getting a different error

the error is as below
-------------------------------------- \-/
  -/- 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 tmd1.mdcrd 1 2
  Checking coordinates: tmd1.mdcrd

PTRAJ: trajout origihbondtry.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
Segmentation fault
-------------------------------------------------------------------------
 could any one suggest me whats wrong .

thanks in advance
balaji
UOM

_________________________________________________________________
cricket and news. Logon to MSN Video for the latest clips
http://www.exploremyway.com_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber