On Mon, Jul 09, 2007, M. Maeda wrote:
>
> I am compiling AMBER 8 program on the Linux machine.
> In the explicit water model condition, It seemed to be run,
> but the resulted PDB files translated by ptraj were wrong.
>
> It seems some water atoms were recognized as the atoms of
> the protein.
We need more information (but probably not all your files): what is the
*exact* symptom of the problem, that is: what is it makes you conclude that
some water atoms were recognized as the atoms of the protein?
What commands did you give to LEaP to prepare the explicit solvent system?
Did you do something different that what is in tutorial B1?
Try to imagine yourself in the position we are in, and see if you can provide
as much information as you can to narrow down the problem. Generally (and I'm
writing this for everyone), just saying that something was "wrong" is of
little help.
....regards....dac
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Received on Wed Jul 11 2007 - 06:07:26 PDT
