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.O
acceptor mask :1-40.N : 1-40.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.O
Mask [:1-40.O] represents 1260 atoms
PTRAJ: acceptor mask : 1-40.N :1-40.H
Segmentation fault
-------------------------------------------------------------------------
could any one suggest me whats wrong .
thanks in advance
balaji
UOM
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Received on Fri Jun 05 2009 - 01:12:52 PDT
