VMD-L Mailing List

From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Tue Jul 21 2009 - 15:24:30 CDT

Sorry all, I found info from VMD tutorial. I promise I will read through the
tutorial next time and stop spamming the mailinglist...
I had the problem because I did namd simulation using amber parameters, but
in order to load DCD file I need to create a psf file after I get the
trajectory.

Thank you!

On Tue, Jul 21, 2009 at 4:05 PM, Yi Shang <mirandaisbest_at_gmail.com> wrote:

> I just realized maybe there isn't any atom/residue name info or things like
> that. But, does that mean we wont visualize DCD trajectory like AMBER ones?
>
>
> On Tue, Jul 21, 2009 at 3:59 PM, Yi Shang <mirandaisbest_at_gmail.com> wrote:
>
>> Hi all,
>> I have been using VMD for like 1 year looking at PDB files or AMBER files,
>> haven't had any problem. It's VMD 1.8.6 downloaded from VMD website.
>>
>> Now I try to learn visualizing DCD files.
>>
>> I downloaded equilibration.dcd from vmd tutorial web page. loaded it into
>> VMD.
>> It said it used plugin dcd, and then finished with equilibration.dcd
>> file.
>> -I saw nothing on the screen.
>> -I went to 'representation' and clicked 'creat rep' (not like PDB files,
>> VMD did not create a representation for that DCD file).
>> Then I saw a box of atoms, represented by small white balls.
>> But I could not change representations, The only combination worked was
>> 'selected atoms: all, Drawing Method: Line or Licorice'.
>> -I tried extension - analysis - sequence viewer, then VMD would crash
>> immediately telling me it encountered some problem and needs to close...
>>
>> Do I need extra plugin to visualize DCD files? I am confused.
>>
>> --
>> Miranda
>>
>
>
>
> --
> Miranda
> 

-- 
Miranda