[AMBER] Simple NAB script from manual segfaults at call to md()

From: Chris King <chrisk1.uw.edu>
Date: Wed, 16 Feb 2011 14:35:26 -0800

I am attempting to run a simple NAB script that loads a single glycine
residue pdb file, minimizes it with conjugate gradient, them runs 1000 steps
of molecular dynamics, all in gas phase.

My script is nearly verbatim the same as the sample NAB script in the
AmberTools manual section about running MM and MD.

After compiling with no errors, the script runs until it gets to the md
step, at which point it segfaults; that is, there is some error with calling
the md() function.
The same behavior occurs with different input PDB's.

Can anyone please help?? Many thanks!

Chris King
Baker Lab
University of Washington

Here is the output:
Running: /work/chrisk/amber11/bin/teLeap -s -f
-I/work/chrisk/amber11/dat/leap/prep -I/work/chrisk/amber11/dat/leap/lib >
Reading parm file (tprmtop)

    mm_options: cut=25.0
    mm_options: ntpr=10
    mm_options: nsnb=999
    mm_options: gamma_ln=5.0
      iter Total bad vdW elect nonpolar genBorn
ff: 0 3.28 3.21 0.71 -0.64 0.00 0.00
ff: 10 -0.06 0.81 0.91 -1.78 0.00 0.00
ff: 20 -0.19 0.87 0.98 -2.03 0.00 0.00
ff: 30 -0.21 0.85 1.08 -2.14 0.00 0.00
    mm_options: tautp=0.4
    mm_options: temp0=100.0
    mm_options: ntpr_md=10
    mm_options: tempi=50.
Segmentation fault

Here is the script:

//calc 100 md steps
molecule m;
float m_xyz[ dynamic ], f_xyz[ dynamic ], v[ dynamic ];
float dummy[2], energy, dgrad;
int minwin;

m = getpdb_prm( "gly.pdb", "leaprc.ff99SB", "", 0 );
allocate m_xyz[ 3*m.natoms ]; allocate f_xyz[ 3*m.natoms ];
setxyz_from_mol( m, NULL, m_xyz );

mm_options( "cut=25.0, ntpr=10, nsnb=999, gamma_ln=5.0" );

mme_init( m, NULL, "::ZZZ", dummy, NULL );
dgrad = 0.1;
minwin = conjgrad( m_xyz, 3*m.natoms, energy, mme, dgrad, 10.0, 100 );

mm_options( "ntpr_md=100, tempi=100.0, temp0=100.0" );
//run md, 1step
md( 3*m.natoms, 100, m_xyz, f_xyz, v, mme );
setmol_from_xyz( m, NULL, m_xyz );
putpdb( "qq.pdb", m );
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Received on Wed Feb 16 2011 - 15:00:04 PST
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