[AMBER] ERROR - No pdb file generated using NAB

From: Andre Serobian <a.serobian.unsw.edu.au>
Date: Sat, 9 Jul 2011 14:08:18 +1000

Hi All,

Ok, got nab to run without errors, however it does not create the pdb file.


nab file:
..........................................................................................................................................
molecule m;
bounds b;
string seq, cseq;
float fret, xyz[ 10000 ];
int ier;

seq = "atgcat";
cseq = wc_complement( "atgcat", "", "dna" );
m = wc_helix( seq, "", "dna", cseq, "", "dna", 2.25, -4.96, 36.0, 3.38, "" );
b = newbounds ( m, "");

useboundsfrom(b, m, "1:1,5:??,H?[T]",getpdb( "/usr/local/amber11/dat/dgdb/basepairs/at.XXIII.pdb" ),"::??,H?[T]",0.1);
useboundsfrom(b, m, "1:2,6:??,H?[T]",getpdb( "/usr/local/amber11/dat/dgdb/basepairs/ta.XXIII.pdb" ),"::??,H?[T]",0.1);
tsmooth(b, 0.0005);

dg_options( b, "gdist=1, ntpr=50, k4d=2.0, randpair=10.0" );
embed( b, xyz );
ier = conjgrad( xyz, 4*m.natoms, fret, db_viol, 0.1, 10.0, 500 );
setmol_from_xyzw( m, NULL, xyz );
putpdb( "nuc.pdb", m, "-wwpdb" );
..........................................................................................................................................




even the following tutorial file from the Amber site does not produce a pdb file:
..........................................................................................................................................
molecule m;

m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb");
..........................................................................................................................................


now it looks like an NAB problem, what would cause this?


Kind regards,

Andre

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Received on Fri Jul 08 2011 - 21:30:03 PDT
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