Mnimization with Cartesian restraints on the heavy atoms of the protein
&cntrl
imin=1, maxcyc=2000,
ntpr=100,
ntr=1,
restraint_wt=0.5,
restraintmask=':473-478'
nmropt=1,
this time kept my md1.in file as above mentioned error msg is
*getting new box info from bottom of inpcrd
peek_ewald_inpcrd: Box info not found in inpcrd
Largest sphere to fit in unit cell has radius = NaN...
*revert plz
On Sat, Jan 2, 2010 at 7:38 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Jan 02, 2010, bharat lakhani wrote:
>
> > ibelly=1, bellymask=:473-478,
>
> > But have got error stating When igb>0, the moving part must be at the
> > start of the molecule. This does not seem
> > to be the case here.
>
> The error message is pretty explanatory here. Consider using NAB for GB
> simulations where you wish to keep large parts of the system fixed.
> Or, you can use restraints (ntr=1) rather than the belly option. Or, you
> may
> be able to rarrange the order of atoms to put the moving portion first.
> For a small moving system in a large environment, the first option may be
> the
> best.
>
> ....dac
>
>
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Received on Mon Jan 04 2010 - 00:30:02 PST
