Dear Amber Users,
I want to calculate normal modes of my
system by NAB using AmberTools12. My input file is like following.
molecule m;
float x[4103], fret;
readparm(m,"protein.prmtop");
mm_options("cut=99., ntpr=50");
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, 0.001, 2000);
// 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, 0, 0, 0.0, 0.0, 0);
The prmtop file given here is made from xleap of AMBER9. Whenever I
run NAB some errors are coming and run stops. The errors are-
Reading parm file (protein.prmtop)
title:
Parameter topology includes 10-12 terms:
These are assumed to be zero here (e.g. from TIP3P water)
Segmentation fault
I think some problem in prmtop file. But what is it I can't
understand. So, please let me know what the errors are and what should
I do.
Sanjib
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Received on Wed Sep 05 2012 - 06:30:04 PDT
