VMD-L Mailing List

From: David Gae (ddgae_at_ucdavis.edu)
Date: Sat Mar 03 2018 - 14:03:09 CST

Dear Wenze Gu,

Maybe this might help.
In AmberTools you can try to do:
cpptraj -p file.parm7 -y traj1.crd -x traj1.nc

then view your simulation in VMD.

David

> On Mar 3, 2018, at 8:52 AM, Gu, Wenze <wenze_gu_at_brown.edu> wrote:
>
> Hi list,
>
> I have a mdcrd file from AMBER. I first loaded the prmtop file as PARAM7, then I loaded the mdcrd file as AMBER COORDS. The mdcrd file is not in NetCDF format (and NetCDF is not an option for reading files in my VMD). However, VMD returns:
>
> Info> Using plugin crd for coordinates from file <path>.mdcrd
> Problem reading CRD file
> Finished with coordinate file <path>.mdcrd
>
> What is causing this problem? Thank you!
>
> Best,
> Wenze Gu
> Department of Chemistry
> Brown University