VMD-L Mailing List

From: Alex Nazlidis (nazlidisalex_at_gmail.com)
Date: Mon Apr 05 2021 - 19:10:18 CDT

Hmmm. I don't know. I get a window pop-up which says "Unable to load
molecule" and the command line says writes:

vmd > corplugin) Error opening file: improperly formatted line.
ERROR) Could not read file ...

Anyways, 1.9.3 does the job, just wanted to let John and the community
know.

Best,
Alex

On Mon, Apr 5, 2021 at 7:18 PM 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!oHmKoKyrGmKLpAUKSfX9cJrEnMgW4wTpsFw-BFUFyatdQmFR_b_lfEWBnyQY9mFzww$
>> <https://urldefense.com/v3/__https://charmm-gui.org/?doc=archive&lib=lipid__;!!DZ3fjg!oNd9thPtnN-jEwHzqvYPFF9NdoOjK6HwenLVkZW_HXwQFTWr6O2juYPoUEcjz9ru6g$>
>> I used to import the .crd molecules by "New molecule->select the .crd
>> file->change the determine file type to CHARMM coordinates" and I could
>> load the molecule.
>>
>> Best,
>> Alex
>>
>> On Mon, Apr 5, 2021 at 4:33 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>>> Hi,
>>> What OS/platform are you running on, and which ".crd" file format
>>> are you referring to (there are several)?
>>>
>>> Best,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Mon, Apr 05, 2021 at 04:31:11PM -0400, Alex Nazlidis wrote:
>>> > Hi all.Ā
>>> > I noticed that the new versions of VMD 1.9.4 won't let me open .crd
>>> files
>>> > unlike VMD 1.9.3 which does. Is there any way to open .crd files in
>>> > 1.9.4?Ā
>>> > Best,
>>> > Alex
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/
>>> <https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!HXCxUKc!mKjp_hxU6H0PEQmcLsQ0vjFn7uv5gcSx3jnEWjZsPoQUP0DcuiiWmg8evUVHxuw$>
>>> Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>> <https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!HXCxUKc!mKjp_hxU6H0PEQmcLsQ0vjFn7uv5gcSx3jnEWjZsPoQUP0DcuiiWmg8e-aJOzd4$>
>>>
>>>
>>
>> --
>> Josh Vermaas
>> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biologyvermaasj_at_msu.eduhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/
>>
>>
> --
> Josh Vermaas
> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biologyvermaasj_at_msu.eduhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/
>
>