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
Received on Thu May 08 2014 - 05:00:04 PDT
