VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Apr 05 2021 - 18:18:20 CDT

Hi Alex,

Is there an error message that gets printed? I can load your example just fine, so it may be a windows-specific issue.

-josh

On 4/5/21 5:49 PM, Alex Nazlidis wrote:
Yeah, I've been changing the default AMBER coordinates to CHARMM coordinates to load them. Essentially, every .crd file that I'm trying to load is failing but here's one for your reference.

Thanks,
Alex

On Mon, Apr 5, 2021 at 5:37 PM Vermaas, Josh <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
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!pSgZYjdxTksAZvLdAcRwZq-x3yq_YL9t2PkJz9p4lX8SenNE_7fEYBQv1tUuOcHiRA$ <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/$>           Phone: 217-244-3349
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--
Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!pSgZYjdxTksAZvLdAcRwZq-x3yq_YL9t2PkJz9p4lX8SenNE_7fEYBQv1tVupBuMmg$ 
--
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!pSgZYjdxTksAZvLdAcRwZq-x3yq_YL9t2PkJz9p4lX8SenNE_7fEYBQv1tVupBuMmg$