You were right.
I added the following line before mme:
setxyz_from_mol( m, NULL, m_xyz );
Now I get
Reading parm file (test.prmtop)
title:
MW6
mm_options: cut=999.0
mm_options: ntpr=1
mm_options: nsnb=999
mm_options: gb=0
bond: 0.993095839
angle: 0.534377553
dihedral: nan
enb14: -0.420260154
eel14: -1729.528969821
enb: -0.011051911
eel: 1109.552505613
egb: 0.000000000
econs: 0.000000000
esurf: 0.000000000
Total: nan
frms: nan
mme returns nan
Now only dihedral gives 'nan'. According to the calculation of Sander, it
should be ~1.2.
On Wed, Jul 28, 2010 at 6:19 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> It may explain why energy calc fails, if your array of
> coordinates is not initialized.
>
> > Initially, I wanted to calculate normal modes but I encountered the
> > problem. So, the original code was cut to narrow down the problem. You
> can
> > ignore the unnecessary steps.
>
> > On Wed, Jul 28, 2010 at 5:49 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > > allocate m_xyz[3*m.natoms];
> > > > allocate f_xyz[3*m.natoms];
> > >
> > > I've never used NAB, but from what you sent it is not clear
> > > that these arrays are ever populated.
>
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>
--
Best,
InSuk Joung
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Received on Wed Jul 28 2010 - 16:30:03 PDT
