VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 17 2011 - 05:56:15 CDT
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On Tue, May 17, 2011 at 5:17 AM, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:
> 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
by adding the necessary capability to the
amber parmtop molfile plugin. only a small
number of plugins can read or write angle and
dihedral information.
axel.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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