VMD-L Mailing List

From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Thu Oct 27 2005 - 16:33:25 CDT

Thanks John! I used psfgen and it works for this sub-structure
selection case. I loaded the original psf file, and the pdb for the frame I am
interested in. I used delatom to delete the atoms I didn't want and then
used writepsf and writepdb.
Ravi

------------------------------------------------------------
On Thu, Oct 27, 2005 at 01:15:39PM -0500, John Stone wrote:
>
> Hi,
> 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
> vmd_at_ks.uiuc.edu
>
> 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