VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 20 2012 - 15:15:31 CDT

On Mon, Aug 20, 2012 at 9:13 PM, Joaquim Rui de Castro Rodrigues
<joaquim.rodrigues_at_ipleiria.pt> wrote:
> Dear VMD users,
>
> I am trying to write a psf with the following commands:
> mol new complex.pdb
> set sel [atomselect top all]
> $sel writepsf test1.psf
>
> psfplugin) WARNING: PSF file is incomplete, no angles, dihedrals,
> psfplugin) impropers, or cross-terms will be written.
> Info) Opened coordinate file test1.psf for writing.
> Info) Finished with coordinate file test1.psf.
>
> However, the psf does not contains bonds.

yes, and rightfully so, since the pdb file contains no bonds.

> Strangely, if I add a random bond with the mouse, and then delete it, VMD outputs all the bonds.

yes. if you manually add or delete a bond, you trigger
a flag that tells VMD that bond information is deliberate
and not just heuristically.

> Is this expected?

yes.

> How can I force VMD to write bonds without having to add/delete a bond?

you cannot simply force it, but you can automate the heuristic
bond generation process so that the bonds are considered deliberate.
check out the procedure here and adapt it as needed.:
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1

cheers,
    axel.

> This is with VMD 1.9.1, on a Mac (OS X 10.5.8)
> Thanks,
> Rui Rodrigues
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.