have you tried using leap to build the prmtop for the vacuum calculation?
if that doesn't work, let us know the specific error message you get
from sander, it's hard to help if you just say it doesn't work.
On Wed, Oct 22, 2008 at 12:11 PM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
>
> Dear Amber users,
>
> I stripped water from a restart file using ptraj and I did the same with the
> topology file using rdparm.
>
> I tried to run an MD simulation of my solute in vacuum but sander failed
> to read the modified restart file
>
>
> any feedback please
>
> best wishes
> Fatima
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Received on Wed Oct 22 2008 - 19:59:02 PDT
