From: John Stone (
Date: Thu Oct 27 2005 - 13:15:39 CDT

  The PSF plugin in VMD doesn't write a complete PSF, as VMD 1.8.3 doesn't
preserve the bonds/angles/dihedrals/impropers when it loads a PSF file.
The VMD 1.8.4 test versions will write bond information now, but they
still don't internally store the angles/dihedrals/impropers to be written
back out later on. This may change for a subsequent version, but that's
the way it is for VMD 1.8.3/4. In order to build a PSF for the
selected sub-structure, you're going to have to use psfgen, or perhaps
the "autopsf' plugin in the 1.8.4 test version, one of those should work fine.

  John Stone

On Thu, Oct 27, 2005 at 04:07:50AM -0700, Ravinder Abrol wrote:
> Hi All,
> I am getting the following error when I use writepsf:
> -------------------------------------------------------------------------
> psfplugin) WARNING: PSF file is incomplete, no bonds, angles, dihedrals,
> or impropers will be written.
> Info) Opened coordinate file subset.psf for writing.
> ERROR) write_timestep returned nonzero
> Info) Finished with coordinate file subset.psf
> ------------------------------------------------
> Here is what I did to achieve my goal of selecting a subset of atoms
> from a frame and writing the pdb and psf file for that subset of atoms
> to restart MD only for them:
> 1) I loaded my original psf file using molecule file browser.
> 2) I loaded my dcd file using load data into molecule option.
> 3) I selected a subset of atoms (not the full list) from a frame using the
> TkConsole window through the command:
> set sel100 [atomselect top "all not ......" frame 100]
> 4) Then I tried to write a psf file for the selected atoms only using:
> $sel100 writepsf subset.psf
> and got the error mentioned above.
> writepdb works fine but writepsf doesn't. Am I missing any steps
> or doing something wrong?
> Thanks very much,
> Ravi

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