It looks like your system is using a rectangular box. If this is the
case try using "image center" instead of "image center familiar". I'm
not 100% sure but I think the 'familiar' keyword is only for truncated
octahedral boxes.
-Dan
On Sun, Sep 19, 2010 at 10:57 AM, bingbing zhang
<zbingbing.ruc.gmail.com> wrote:
> Dear,
>
> I am using AMBER9 to equilibrate and run production dynamics on a protein.
> Everything seems normal during the equilibration progress, but the PDB files
> generated by "trajout" have some problems. I run the MD simulation with
> "iwrap=1".
>
> Form figure1, the picture of one of these PDB files, it is obvious to
> find that the protein is at the edge of the box and some atoms stay outside
> the water TIP3P box. It seems like there is a big ball-like thing in the
> space.
>
> So I try adding " center :1-150" and " image center familiar" to the
> ptraj file to locate the solute molecule into box. Then I get the figure2
> and 3, picture of new pdb file. In the new pdb, the water molecules are not
> homogeneous. I want to get two or more box show in pdb, but I don't know how
> to get it.
>
> Does someone have any suggestion to overcome the problems?
>
> Looking forward to getting your help!
>
> Thank you very much in advance!
>
>
> Best Regards
>
> Zhang Bingbing
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 21 2010 - 08:00:10 PDT
