Dear Amber user,
Am trying to calculate the raman vibrational frequancy of (C-O) of a macromolecule , using the script below in file G17-vac-nmde.in:
molecule m;
float x[1080], fret;
m = getpdb("G17-vac-min.pdb");
readparm(m, "G17-vac.top");
getxyz("G17-vac-min.rst",360,x);
mm_options("cut=999, ntpr=10, 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,0.1,0.001,2000);
//newton-raphson minimization
newton(x,3*m.natoms,fret,mme,mme2,0.00000001,0.0,6);
//get normal modes
nmode(x,3*m.natoms,mme2,50,0,0.0,0.0,0);
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First qusetion:whem i submit this job using nmode function (as in the job script (myscript-vac-nmode.sh ) gave me an error in file myscrip-vac-nmode.sh.e36040 could some one tell me what is wrong and how to fix it please.
second: the
second question mme2,50,0,0.0,0.0,0 what it refer for
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Received on Tue Feb 26 2013 - 09:00:03 PST
