Thanks!
//the code:
molecule m,mi;
int ier;
float m_xyz[dynamic], f_xyz[dynamic],v[dynamic];
float dgrad, fret, dummy[2];
mi = bdna("gcgc");
putpdb("temp.pdb", mi);
m=getpdb_prm("temp.pdb", "leaprc.ff94SB","",0);
allocate m_xyz[ 3*m.natoms ];
allocate f_xyz[ 3*m.natoms ];
allocate v[ 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);
fret = mme(m_xyz, f_xyz, 1);
printf("Initial energy is %8.3f", fret);
dgrad = 0.1;
ier=conjgrad(m_xyz, 3*m.natoms, fret, mme, dgrad, 10.0, 100);
setmol_from_xyz(m,NULL,m_xyz);
putpdb("gcgc.min.pdb",m);
mm_options("tautp=0.4, temp0=100.0, ntpr_md=10, tempi=50.");
md(3*m.natoms, 1000, m_xyz, f_xyz, v, mme);
setmol_from_xyz(m, NULL, m_xyz);
putpdb("gcgc.md.pdb",m);
On Wed, Jan 20, 2010 at 10:27 AM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jan 20, 2010, Lixia Jin Day wrote:
>
> > Running: /usr/local/amber11/bin/teLeap -s -f
> > leap.in-I/usr/local/amber11/dat/leap/cmd
> > -I/usr/local/amber11/dat/leap/parm
> > -I/usr/local/amber11/dat/leap/prep -I/usr/local/amber11/dat/leap/lib >
> > tleap.out
> > Reading parm file (tprmtop)
> > tprmtop, tprmtop.Z: does not exist
> > Cannot read parm file tprmtop
>
> Can you post the code you are trying to run? It's certainly possible that
> there is some glitch in the manual.
>
> You don't need Amber for this, and the message above is not related to
> that.
> But we need more information in order to help.
>
> ...dac
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 20 2010 - 10:00:02 PST
