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!
But when I use the pdb and .prmtop files of one Alanine molecule generated
by Amber software, the NAB analysis can pass smoothly. So does anyone can
tell me why the above NAB script doesn't work? The pdb and prmtop files I
used for melamine are attached.
Thanks a lot in advance.
Best!
Dongshan
--
---------------------------------------------------------
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 - 02:30:04 PDT
