VMD-L Mailing List

From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Thu Oct 27 2005 - 06:07:50 CDT

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