Hello,
If you are trying to run either an implicit solvent or vacuum
simulation, you should set ntb=0. I believe it defaults to ntb=1, in
which case I believe sander will search for box information in the
inpcrd file. Also, these restraints are not being placed only on the
heavy atoms, it's being placed on all atoms in residues 473-478 as I
understand it.
Finally, nmropt and ntr are different, so if you don't want to add any
nmr restraints (just the cartesian reference restraints), then set
nmropt=0.
Good luck!
Jason
On Mon, Jan 4, 2010 at 3:10 AM, bharat lakhani <lakhbharat.gmail.com> wrote:
> 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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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 04 2010 - 05:00:04 PST
