Re: [AMBER] NAB problem with a metallic atom

From: InSuk Joung <i.joung.gmail.com>
Date: Wed, 28 Jul 2010 19:16:46 -0400

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
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