From: Jorgen Simonsen (
Date: Tue May 17 2011 - 04:17:33 CDT

Hi all

I have an earlier thread but I seem to get the same problems as
described earlier but the solution does not seem to work or I have
understand it correctly.

I load my new.prmtop into vmd

vmd -dispdev text new.prmtop

which is fine but it is not able to read bond or angle information

Info) Atoms: 14321
Info) Bonds: 14324
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 4745
Info) Waters: 4738

Then I try different approaches

mol new test.prmtop waitfor all
animate dup 0
set sel [atomselect top all]
$sel writepsf myfile.psf

atomsel: frame -1 out of range for molecule 1

How to resolve this thanks in advance