From: Peter Freddolino (
Date: Sat Feb 05 2022 - 18:27:49 CST

Hi Kelly,
Those indicates are automatically appended to your prefix by autopsf to
specify the various outputs that are generated. If you want to change them,
by far the easiest solution is just to add to your script something like
file rename PREFIX_autopsf.psf {WHATEVER YOU WANT}
and so on for the other generated files. See the tcl documentation on the
`file rename` command for details:*M30__;Iw!!DZ3fjg!qbNJPhAZD99dfNUlSgSa4oeaoyuEYCMRhnKcGagVZzwk9IRV5fOZ09-22FmxgbriHQ$
You can also change the autopsf source to change the names, but that is
probably more trouble than it is worth, and a permanent solution for a
temporary problem.

On Sat, Feb 5, 2022 at 7:24 PM McGuire, Kelly <> wrote:

> I am using autopsf through the console. I would like to get rid of the
> words "formatted" and "autopsf" in the final name for both the pdb and
> psf. I use -prefix, but those words still show up. How do I get rid of
> them? I am using VMD 1.9.3 in this case.
> *Dr. Kelly L. McGuire*
> *PhD **Biophysics*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*