Hi Hannes,
Many thanks for identifying my error.
It works now.
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
On Sat, Jun 6, 2015 at 12:02 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> '–' and '-' are two different characters. The first is an endash but you
> want to use the latter that is a simple ASCII minus just as in the usage
> message.
>
> ________________________________________
> From: Michael Shokhen [michael.shokhen.biu.ac.il]
> Sent: 06 June 2015 09:24
> To: AMBER Mailing List
> Subject: [AMBER] Error unknown flag: –O
>
> Dear Amber List members,
>
> I have a work station and server with ubuntu linux.
> There are amber14 and ambertools15 installed on both computers
> according to the manual directions. All tests on sander. pmemd.mpi, and
> pmemd.cuda were successful.
> I have been running without problems different amber tutorials
> as well as some of my tasks.
> Suddenly couple of days ago I faced a strange error message on both of my
> computers
> responding on a command that was used previously without any problem (see
> below).
> Analogous respond was on sander, pmemd, and pmemd.mpi commands.
>
> I would appreciate any advise how to solve the problem.
>
> Thank you,
> Michael
>
> shokhen.shokhen-lnx:~/Documents/amd_amber/1_$ pmemd.cuda –O –i min1.in –o
> min1.out –p ../*.prmtop –c ../*.inpcrd –r sp1_min1.rst –ref ../*.inpcrd &
> [1] 4324
> shokhen.shokhen-lnx:~/Documents/amd_amber/1_$
> unknown flag:
> –O
>
>
> usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo
> -l logfile]
> [-amd amdlog_name -scaledMD scaledMDlog_name -suffix
> output_files_suffix]
>
> STOP PMEMD Terminated Abnormally!
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.gmail.com
> email: shokhen.mail.biu.ac.il
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jun 06 2015 - 03:00:02 PDT
