VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Thu Aug 31 2006 - 17:16:01 CDT

Please help me because I am surely doing something wrong. I am using VMD
1.8.4 under Linux.
I load a both psf and pdb files from the shell for a protein in a water
box.

$ vmd protein.psf protein.pdb

I want to remove all the water so now from the tk console I put
set prot [atomselect top protein]

$prot writepsf prot.psf
$prot writepdb prot.pdb

Now if I take a look the psf from the shell
$ grep angles protein.psf
66246 !NTHETA: angles
$ grep angles prot.psf
0 !NTHETA: angles

So, the angles have magically disapeared. The same happens to the
dihedrals and impropers.
Is this a bug or are there some steps that I am missing?

Regards
Cesar