VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 27 2005 - 13:15:39 CDT

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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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