AMBER Archive (2006)

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

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Sat Dec 16 2006 - 12:35:13 CST

Here is a strategy that might yield success -

1) Use ptraj to output a series of .pdbs from your .crd file. If that
does not create useful .pdbs, something is fundamentally in disagreement
between your prmtop and crd files, as Dr. Simmerling has suggested. If
you get reasonable pdb snapshots, then on to #2 ->

2) You might try using chimera or mddisplay or molview etc to visualize
your trajectory. These may not give you the movie-making power of vmd.
But, if they work, you will be well positioned for #3 ->

3) Write the authors of VMD directly with details of your success
everywhere else.

Chris

> 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
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>
>
>
> --
> Live Life; Don't pass it
> Bertrand.P.S.Russell
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu