AMBER Archive (2006)

Subject: Re: AMBER: How to make a movie with .crd files in VMD?

From: bertrand russell (betrussell23_at_gmail.com)
Date: Sat Dec 16 2006 - 11:35:16 CST

Hello Simmerling,

                                I loaded the .pdb file as the reference and
.crd file (not the .rst file) which contains 250 frames. I used the AMBER
coordinates with box for the both ( .pdb and .crd). Would it be a problem,
since I used ntx=1 in my simulation? If so, I am expecting your help to how
to solve this problem. Many thanks for your reply.

On 12/16/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
>
> make sure you use the right prmtop for the crd file and
> also make sure you choose either AMBER coordinates
> or AMBER coordinates with box. By crd file you do mean the
> mdcrd file from sander, not a restart file, right?
>
> bertrand russell wrote:
>
> > Dear AMBER users,
> >
> > I am trying to make a movie in VMD using amber .crd files. I loaded
> > the initial .pdb file. Then I followed the following commands. But my
> > protein is moving randomly, I am sure that is not the movie what I am
> > trying to make.
> >
> > >file > new molecule > i browsed and loaded the molecule
> >
> > >file > load data into molecule > I browsed and loaded the .crd file
> >
> > > extensions > visualization > movie maker
> >
> > I clicked the movie make button. I tried to make movie by changing the
> > renderer settings and movie settings. But I am not getting any movie
> > rather I am getting very random motion of my protein. While doing
> > simulation I gave ntx=7 and my .crd file consists of 250 frames. Could
> > anyone help me to make a movie with detailed description since this is
> > the first time I am trying to make a movie.
> >
> > Thanks a lot in advance.
> >
> > --
> > Live Life; Don't pass it
> > Bertrand.P.S.Russell
>
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-- 
Live Life; Don't pass it
Bertrand.P.S.Russell

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