AMBER Archive (2007)

Subject: Re: AMBER: amber md movie using Chimera

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Wed Sep 05 2007 - 13:04:57 CDT

Since you stripped water and ions from the trajecotry file, you need a
new topology without those molecules to match the new traj file.

On Wed, 2007-09-05 at 12:42 -0500, Wang, Xuelin wrote:
> Dear amber users:
>
>
>
> I have a problem to make an Amber MD movie using Chimera. I am sure I
> used the right Amber top file and mdcrd file, since I can use VMD to
> display them. In my trajectory file, I already striped water and
> counter-ions. Only box information was left with trajectory. However,
> when I display trajectory, all trajectories were out of shape. I saw
> the similar thing when I used VMD to display the trajectory without
> including PBC option. I doubt that there is something wrong with box
> information. But I don’t know how to fix it. Any ideas?
>
>
>
> Thanks
>
> Xuelin
>
>
>
>

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