VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Thu Jul 23 2009 - 09:21:20 CDT

vmd -parm7 myamberparmfile.top -dcd mynamdtrajectory.dcd
or

vmd -parm myamberparmoldformat.top -dcd mynamdtrajectory.dcd

'nuff said!

Tom
On Tuesday 21 July 2009, Yi Shang wrote:
> 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 

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Thomas C. Bishop     *
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