try using the prmtop, not the pdb file.
bertrand russell wrote:
> 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.csb.sunysb.edu
> <mailto:carlos.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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Received on Sun Dec 17 2006 - 06:07:33 PST
