Hello,
As was mentioned in the previous email, I think you need to use either a
rectangular box or a truncated octahedron for PBC. In any case, periodic
boundaries for spheres are not well defined as far as I know.
Good luck,
Jason
On Mon, Oct 18, 2010 at 12:19 PM, balaji nagarajan <balaji_sethu.hotmail.com
> wrote:
>
> Dear amber !
>
> I have solvated a peptide with the solvent using packmol
> the solvent (organic ) is not in the amber library .
>
> I have enclosed the peptide in the solvent sphere .
>
> Now I tried minimising the system with ntb=1 ,
>
> but the minimization stopped , when i gave the ntb=0 , the minimization was
> done .
>
> This is also the same problem like the solvateshell ? as i earlier asked
> or else it is possible to fix the
> periodic boundary for a sphere ?
>
> I would like to know the interaction between the solvent and the
> solute is it possible to do in amber ?
>
>
> thanks in advance
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 18 2010 - 10:00:03 PDT
