Re: [AMBER] Error unknown flag: O

From: <hannes.loeffler.stfc.ac.uk>
Date: Sat, 6 Jun 2015 09:02:05 +0000

'' 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
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Received on Sat Jun 06 2015 - 02:30:03 PDT
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