AMBER Archive (2006)

Subject: Re: AMBER: Problem with ptraj

From: Gobind Singh Bisht (gsbisht1_at_gmail.com)
Date: Fri Sep 08 2006 - 23:35:28 CDT

Hi all,
       I think i found the solution to my problem. Since i was using amber
on cygwin platform, problem occured due the file being written on a windows
progam. However the script worked when i wrote the same script in xemacs.
thanx anyways

On 9/9/06, Gobind Singh Bisht <gsbisht1_at_gmail.com> wrote:
>
> 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/
> 

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