Yes, Unfortunately I could not use any of the tutorials, since I encounter some errors regarding them while I am sure about my Amber installation.
I run the code which is mentioned in the bellow website:
http://ambermd.org/tutorials/basic/tutorial1/section6.htm
but when I run the code: ./a.out
I encounter error and I got no a-dna.nab.pdb files in my directory :( and in spite, by this code $AMBERHOME/bin/nab a-dna.nab I get the a.out and a-dna.c files in my directory!!!
Are these codes really compatible with Amber tools 15??? :-/
Excuse me for talking a lot.
Bests
________________________________________
From: Marcelo Andrade Chagas [andrade.mchagas.gmail.com]
Sent: Tuesday, February 23, 2016 12:22 AM
To: david.case.rutgers.edu; AMBER Mailing List
Subject: Re: [AMBER] No exe file in Amberhome
Dear AMBER list
maybe the problem has already been solved
but follow links to tutorials that have been using to install ambertools15
The first relates to install mode of mpi compiler to amber
in parallel, which must be the same as is used to install amber
(If used gnu):
http://lsi.ugr.es/~jmantas/pdp/ayuda/datos/instalaciones/Install_OpenMPI_en.pdf
The second relates to the steps of instação ambertools15, for example:
http://jswails.wikidot.com/installing-amber14-and-ambertools14
Best regards
Marcelo
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-02-22 18:03 GMT-03:00 David A Case <david.case.rutgers.edu>:
> On Mon, Feb 22, 2016, Mahdieh Hadi wrote:
>
> > http://ambermd.org/tutorials/basic/tutorial3/section1.htm
>
> fixed now; thanks for the report.
>
> > and unfortunately, I have the same problems with
> > commands in the Amber 15 manual and this site "
> > http://ambermd.org/tutorials/basic/tutorial1/section2.htm". I could not
> > simulate the duplex DNA with the command:
>
> > molecule m;
> > m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
> > I encounter this error, -bash: syntax error near unexpected token `('
>
> These are lines that you put into a program.nab file, then compile using
> nab.
> You can't just type them in the SHELL.
>
> >
> > I really appreciate it if you could provide me with an up to dated
> > manual or site, so I could work with Amber tools15.
>
> Just go to http://ambermd.org/#AmberTools, scroll down a bit and click on
> "Download AmberTools15".
>
> ...good luck....dac
>
>
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Received on Tue Feb 23 2016 - 00:00:03 PST
