Hi Jason,
Thanks for your prompt reply. I changed the input file name from mel.nab to
mmm.nab so I got the error info.
It's strange it works in your computer. Which Amber version you use? I use
Amber 12.
Best!
Dongshan
On Thu, May 8, 2014 at 7:56 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2014-05-08 at 17:23 +0800, Dongshan Wei wrote:
> > Dear Amber Users,
> >
> > I want to use NAB to do normal mode analysis for one melamine molecule in
> > vacuum. After I generated the mel.pdb file by hand and the force filed
> file
> > mel.prmtop by R. E. D. server, I try to use the following NAB script
> > (mel.nab) to do normal mode analysis:
> >
> >
> ************************************************************************************************
> > molecule m;
> > float x[4000], fret;
> >
> > m = getpdb( "mel.pdb" );
> > readparm( m, "mel.prmtop" );
> > mm_options( "cut=999., ntpr=50, nsnb=99999, diel=C, gb=0, dielc=1.0" );
> > mme_init( m, NULL, "::Z", x, NULL);
> > setxyz_from_mol( m, NULL, x );
> >
> > // conjugate gradient minimization
> > conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.00001, 20000 );
> >
> > // Newton-Raphson minimization\fP
> > mm_options( "ntpr=1" );
> > newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 6 );
> >
> > // get the normal modes:
> > nmode( x, 3*m.natoms, mme2, 30, 0, 0.0, 0.0, 0);
> >
> >
> ************************************************************************************************
> >
> > When I preformed "$AMBERHOME/bin/nab mel.nab", the below error message
> > always occurs:
> >
> > mmm.nab:21 syntax error
> > nab2c failed!
>
> This doesn't make sense to me. You said you ran the command
>
> $AMBERHOME/bin/nab mel.nab
>
> but the error message says that "mmm.nab" has a syntax error (around
> line 21 of mmm.c). Why the different name?
>
> Also, if I download your attached files and copy-and-paste your program
> above to "mel.nab", I run the command
>
> nab mel.nab
>
> and I get a program a.out that runs without error. I'm not sure what
> problems you are having, but I cannot reproduce them.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------
Dongshan Wei, Dr.
Chongqing Institute of Green and Intelligent Technology, CAS
266 Fangzheng Ave, Beibei District, Chongqing 400714, China
Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
Phone: (+86) 23-65935641
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Received on Thu May 08 2014 - 05:30:04 PDT
