On Mon, Oct 18, 2010 at 4:28 AM, balaji nagarajan
<balaji_sethu.hotmail.com>wrote:
>
> Dear Amber !
>
> I have a small doubt regarding the solvateshell option
>
Look at the solvateshell option in the AmberTools manual. It says that the
resulting shape will be irregular, since it's really just the shape of the
original molecule (a little smoothed out by adding a solvent buffer).
Irregular shapes are not conducive to periodicity, so I'm pretty sure no box
information is written because no box information CAN be written. As a
result, you have to run non-PBC simulation (i.e. ntb=0). I tried this once
upon a time a long time ago, and you have to use a solvate option that
supports PBC to use constant volume, such as solvatebox or solvateoct.
Good luck!
Jason
>
> I have placed a peptide inside the solvent by giving
>
> solvateshell model TIP3PBOX 10
>
> I generated the .prmtop and .inpcrd files
>
> when i gave the minimization with
>
> &cntrl
> imin = 1,
> maxcyc = 500,
> ncyc = 250,
> ntb = 1,
> igb = 0,
> cut = 12
> /
>
>
> the minimization stoped by saying error
>
>
> | Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info not found in inpcrd
> |Largest sphere to fit in unit cell has radius = 0.000
>
>
> but when i gave the ntb=0 the sander performed minimization .
>
> could any one tell me what the problem is ?
> regards
> balaji
>
>
>
>
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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 Oct 18 2010 - 05:00:04 PDT
