Ok. So I will describe it in detail. I have made a nab file in with the bellow mentioned code:
// Program 1 - Average B-form DNA duplex
molecule m;
m = fd_helix( "adna", "aaaaaaaaaa", "dna" );
putpdb( "a-dna.nab.pdb", m, "-wwpdb");
then I copy it to the amberhome directory. Then I run the bellow code:
$AMBERHOME/bin/nab a-dna.nab
./a.out
and I encountered the bellow error:
dyld: Library not loaded: /Users/mha/amber14/lib/libfftw3.3.dylib
Referenced from: /Users/amber14/./a.out
Reason: image not found
Trace/BPT trap: 5
Bests
________________________________________
From: Hai Nguyen [nhai.qn.gmail.com]
Sent: Tuesday, February 23, 2016 8:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] No exe file in Amberhome
what is the error when you are running ./a.out?
Hai
On Tue, Feb 23, 2016 at 2:51 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Feb 23 2016 - 01:30:04 PST
