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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Received on Sun Sep 10 2006 - 06:07:26 PDT
