VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Feb 05 2022 - 19:22:13 CST

Yep that worked perfectly, thanks!

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Peter Freddolino <petefred_at_umich.edu>
Sent: Saturday, February 5, 2022 5:27 PM
To: McGuire, Kelly <mcg05004_at_byui.edu>
Cc: VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: autopsf question

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: https://urldefense.com/v3/__https://www.tcl.tk/man/tcl/TclCmd/file.html*M30__;Iw!!DZ3fjg!sAgFNEfJ7KmXphi-8yFz_z8YCxXnJaZlAerodLl0PyPGJKFG3_Xj602LAniU9UuReQ$
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.
Best,
Peter

On Sat, Feb 5, 2022 at 7:24 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> 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