VMD-L Mailing List

From: Nuno Ricardo Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Fri Dec 15 2006 - 03:51:01 CST

Hi Bertrand

----- Original Message -----
From: bertrand russell
To: Nuno Ricardo Loureiro Ferreira
Sent: Friday, December 15, 2006 8:07 AM
Subject: Re: vmd-l: How to make movie with .crd files?

<Hai Ferreira,
<
< Thank you very much for your reply. As you said I tried to align protein. But unfortunately I couldn't do that. I <loaded the initial .pdb file of my protein and then I tried to load the .crd file. But I couldn't succeed the attempt.

So, lets start by the beginning.

I wrote some mistakes in my previous email:
When I was refering to "plugin Movie Maker", the plugin is (Extensions.Visualization.Movie Maker) and not (Extensions.Analysis.RMSD *) of course. And vice versa.

What do you want to say with "I couldn't succeed the attempt"?
Were you successfull on reading the trajectory? VMD needs usually 2 files. The topology file (a .pdb this case) should correspond to the trajectory system (same number of atoms, ...). Check this.

Or you weren't successfull using the RMSD calculator?
Are you using the last version of VMD?
<
< Another thing is that, my .crd file has only 250 frames, but while I did the pervious attempt (using load state <command) It was showing me that it read some 2177 frames. What might be the reason for this. Since I am a beginner <in this, in particular making movies and viewing molecules using VMD, it would be of great help if could explain in <somemore detail. Thanks in advance.

About this problem, I read somewhere in the mailing list, a case similar to this, and if I'm not mistaken was also an AMBER trajectory. The user claimed the trajectory should have X frames but VMD read Y frames. Do a search on the mailing list.