AMBER Archive (2006)

Subject: AMBER: Problem with ptraj

From: Gobind Singh Bisht (gsbisht1_at_gmail.com)
Date: Fri Sep 08 2006 - 16:00:19 CDT

Dear amber users,
                    I am trying to use ptraj to analyse hydrogen bonds. but
some error is generated...
my input file:
---------------------------------------------------------------------------------------------------------------------------------------------------------

trajin DNA_melt.mdcrd

donor A N1

donor T O4

donor T O4

donor C N3

donor C O2

donor C O2

donor C5 N3

donor C5 O2

donor C5 O2

donor C3 N3

donor C3 O2

donor C3 O2

donor G O6

donor G O6

donor G5 O6

donor G5 O6

donor G3 O6

donor G3 O6

acceptor T N3 H3

acceptor A N6 H61

acceptor A N6 H62

acceptor G N1 H1

acceptor G N2 H21

acceptor G N2 H22

acceptor G3 N1 H1

acceptor G3 N2 H21

acceptor G3 N2 H22

acceptor G5 N1 H1

acceptor G5 N2 H21

acceptor G5 N2 H22

acceptor C N4 H41

acceptor C N4 H42

acceptor C3 N4 H41

acceptor C3 N4 H42

acceptor C5 N4 H41

acceptor C5 N4 H42

# do the h bond search

hbond series hbond
-------------------------------------------------------------------------------------------------
the output file is:

\-/

-/- PTRAJ: a utility for processing trajectory files

/-\

\-/ Version: "AMBER 9.0 integrated" (April 2006)

-/- Executable is: "ptraj"

/-\

\-/ DC5 DC DG DC DC DA DG DC DG DG

DC DG DT DT DA DA DT DA DC DT

DT DA DA DG DT DA DT DT DA DT

DG DG DC DC DG DC DT DG DC DG

DC DC3 DG5 DG DC DG DG DT DC DG

DC DC DG DC DA DA DT DT DA DT

DG DA DA DT DT DC DA DT DA DA

DT DA DC DC DG DG DC DG DA DC

DG DC DG DG3

PTRAJ: Processing input from "STDIN" ...

PTRAJ:
{\rtf1\ansi\ansicpg1252\deff0\deflang1033{\fonttbl{\f0\fswiss{\*\generator
Msftedit 5.41.15.1507;}\viewkind4\uc1\pard\f0WARNING in ptraj(): No input
trajectories specified (trajin), aborting...

-------------------------------------------------------------------------------------------

 I have checked that the input file DNA_melt.mdcrd is in the $AMBERHOME
directory.

What culd the error be due to????

any suggestions please

thanx in advance 

-- 
Gobind Singh Bisht
Btech III year (Biotechnology and Biochemical Engineering)
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal, India
Ph No: +919932604909
Website: http://users.cjb.net/gobindbisht/

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