VMD-L Mailing List

From: nunolf_at_ci.uc.pt
Date: Thu Dec 21 2006 - 14:22:10 CST

Hi again Rita

Took the freedom to re-send your answer to vmd mailing list, for others
to read.

Offline you told me that you want to save a pdb file from a trajectory
that you
obtained, in order to begin a new simulation (in AMBER) using that pdb as the
template, that's it?

I guess that your trajectory was produced with AMBER. So there's no
problem for
VMD to read the data.
Once you have loaded the data into VMD (you will need a parm and crd
file), you
can save a specific frame from the trajectory in pdb format easily. First
choose the molecule in the VMD main window (just click once with the mouse),
then File/Save coordinates.
There, you can choose the output file type (PDB in your case), as well as the
frame to save Just a remark. The first frame of a trajectory inside VMD is 0.
So if you want frame 50 to be saved, *first* variable == *last* == 49. Do not
worry with the stride (== frame step) var.

Hope this sheds some light to your question.
Feel free if this is not the expected answer.
Cheers,
Nuno

P.S. Brasileira? Pelo alo, tem que ser ! ;-)

Quoting Rita Cassia <Rita.Cassia_at_gmx.de>:

> Yes.
>
> Um abraco
> -------- Original-Nachricht --------
> Datum: Thu, 21 Dec 2006 14:49:55 +0000
> Von: nunolf_at_ci.uc.pt
> An: Rita Cassia <Rita.Cassia_at_gmx.de>
> Betreff: Re: vmd-l: pdb file
>
>> Hi Rita
>>
>> Quoting Rita Cassia <Rita.Cassia_at_gmx.de>:
>>
>> > Dear All,
>> >
>> > i would like to know how i can get a "new" pdb file after a
>> > simulation, using VMD.
>> >
>>
>> What do you mean by a "new" pdb?
>> Do you want to convert your trajectory file to a pdb file, that's it?
>> Cheers,
>> Nuno
>>
>
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