Re: [AMBER] Error message from FEW in Amber14 tutorial A24

From: Michele Bonus <michele.bonus.hhu.de>
Date: Sun, 22 Mar 2015 19:19:28 +0100

Dear Michael,

most probably this issue has its cause in Ubuntu's use of dash (Debian
Almquist Shell) rather than bash or csh as the default shell.

You could try to check the symlink of ~bin/sh, by either
ls -l /bin/sh
which might return "/bin/sh -> dash*"
or
file /bin/sh
which might return "/bin/sh: symbolic link to `dash'".

If the symlink is set to dash for your system, you could alter this to
bash by
ln -sf /bin/bash /bin/sh

Then you could re-run the script and see if it runs through.

Best regards,
Michele

-- 
Michele Bonus
PhD student
Heinrich-Heine-University Düsseldorf
Institute for Pharmaceutical and Medicinal Chemistry
Building 26.23, Level 00, Room 22
Universitätsstr. 1
40225 Düsseldorf
> Dear All,
>
>
>
> I have been trying to follow
>
>
>
> Tutorial A24
>
>
>
> Free energy calculations with the Free Energy Workflow Tool (FEW)
>
> By: Nadine Homeyer and Holger Gohlke
>
>
>
> I used Ubuntu Linux workstation with Bash shell,
>
> where I have academic licensed Amber14 and AmberTools14.
>
>
>
> Adopting the paths changes ( also in leap_am1) as requested in tutorial
>
>   I used the command:
>
>
>
> perl ~/amber14/AmberTools/src/FEW/FEW.pl MMPBSA  /home/shokhen/tutorial/cfiles/leap_am1
>
> The FEW started and aborted with error message:
>
>
>
> ##############################################
>
> #                                                                                          #
>
>
>
> #                                                                                          #
>
>
>
> #                        FEW                                                          #
>
>
>
> #               Free Energy Workflow                                        #
>
>
>
> #                                                                                           #
>
>
>
> #                                                                                           #
>
>
>
> ###############################################
>
>
>
>
>
>
>
>   Checking input parameters and files.
>
>
>
> sh: 1: Syntax error: Bad fd number
>
> Cannot open file log.txt for reading.
>
>
>
> I would appreciate any directions how to solve the problem.
>
>
>
> Thank you,
>
> Michael
>
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Sun Mar 22 2015 - 11:30:02 PDT