VMD-L Mailing List

From: mohamed marzouk (mohamedmarzoukphysics_at_gmail.com)
Date: Tue Apr 06 2021 - 02:50:07 CDT

Sorry for interrupt,
Still no possible way to open .nc files of Amber by VMD on Mac OS Catalina or BigSur?!
I mean using 1.9.4 edition of VMD

Sent from my iPhone

> On Apr 6, 2021, at 8:47, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
>  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> 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!s5chi0xrQB3eGoyJjNKRy3YDE4-8-nyaAVOpPs4IVMiAV8xnifU6CyXnwi369IrE5Q$
>>>> 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> 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
>>>>>
>>>>> 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
>>> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!s5chi0xrQB3eGoyJjNKRy3YDE4-8-nyaAVOpPs4IVMiAV8xnifU6CyXnwi2LbCcFwQ$
>
> --
> Josh Vermaas
> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
> vermaasj_at_msu.edu
> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!s5chi0xrQB3eGoyJjNKRy3YDE4-8-nyaAVOpPs4IVMiAV8xnifU6CyXnwi2LbCcFwQ$