From: Marzieh Alishahi (alishahi.mar_at_gmail.com)
Date: Fri Jan 18 2013 - 00:51:15 CST

hi
try your Basis vectors as follows;

1.444 0.0 0.0
0.0 4.170 0.0
0.0 0.0 4.718

about Cutoff, I think it can be defined according to Bond distance between
AG atoms.
Best,

Marzieh Alishahi

On Fri, Jan 18, 2013 at 1:49 AM, hamid mosaddeghi <hamid592004m_at_yahoo.com>wrote:

> Dear VMD users
>
> I need to add new material to inorganic builder.
>
> but I have problem with define cutoff and Basis vetors.
>
> for exmaple I want to add silver to it. I prepare proper *.pdb and
> *.top file for it.
>
> my pdb of unit cell is:
>
>
> -------------------------------------------------------------------------------------------
> ATOM 1 AG1 AG X 1 0.000 0.000 0.000 1.00 0.00
> UC1 AG 0
> ATOM 2 AG2 AG X 1 1.444 2.502 0.000 1.00 0.00
> UC1 AG 0
> ATOM 3 AG3 AG X 1 0.000 1.668 2.359 1.00 0.00
> UC1 AG 0
> ATOM 4 AG4 AG X 1 1.444 4.170 2.359 1.00 0.00
> UC1 AG 0
> ATOM 5 AG5 AG X 1 1.444 0.834 4.718 1.00 0.00
> UC1 AG 0
> ATOM 6 AG6 AG X 1 0.000 3.336 4.718 1.00 0.00
> UC1 AG 0
> END
>
> -----------------------------------------------------------------------------------------------
>
> for this pdb file how define proper Basis vetors and Cutoff?
>
> thnaks for attention
>
> Hamid Mosaddeghi
>
> Phd Student Of Physical Chemistry
>