VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Apr 05 2021 - 16:37:56 CDT

Hi Alex,

At least on a Linux system with 1.9.4a48, I can open CHARMM-GUI crd files I had previously generated. VMD *did* try to be clever and load them as AMBER coordinates by default, since they also use crd as a file extension, but if you change it to CHARMM coordinates they loaded fine. Do you have an example crd file that is causing you issues?

-Josh

On 4/5/21 4:41 PM, Alex Nazlidis wrote:
I'm using Windows and I'm downloading lipid conformations from CHARMM-GUI: https://urldefense.com/v3/__https://charmm-gui.org/?doc=archive&lib=lipid__;!!DZ3fjg!pOZgE-FpguMV_zH-CnWwmoWJX-IytSf3RjqJskBY52FN3juRFZ334LE59F8VG67BUw$ <https://urldefense.com/v3/__https://charmm-gui.org/?doc=archive&lib=lipid__;!!DZ3fjg!oNd9thPtnN-jEwHzqvYPFF9NdoOjK6HwenLVkZW_HXwQFTWr6O2juYPoUEcjz9ru6g$>
I used to import the .crd molecules by "New molecule->select the .crd file->change the determine file type to CHARMM coordinates" and I could load the molecule.

Best,
Alex

On Mon, Apr 5, 2021 at 4:33 PM John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
Hi,
  What OS/platform are you running on, and which ".crd" file format
are you referring to (there are several)?

Best,
  John Stone
  vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

On Mon, Apr 05, 2021 at 04:31:11PM -0400, Alex Nazlidis wrote:
> Hi all.Ā
> I noticed that the new versions of VMD 1.9.4 won't let me open .crd files
> unlike VMD 1.9.3 which does. Is there any way to open .crd files in
> 1.9.4?Ā
> Best,
> Alex 

--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/$>           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/$>
--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!pOZgE-FpguMV_zH-CnWwmoWJX-IytSf3RjqJskBY52FN3juRFZ334LE59F-LxYsfug$