some of the other replies don't seem to get at the main issue here. VMD in
windows can't read netcdf (binary) format. So what's really going on here
isn't your file name or extension, it may be that you've written to a
binary format which is the default in Amber now (ioutfm=1). If you want,
you can change ioutfm in your mdin file to write ascii trajectories
instead. However, they are larger and lower precision. cpptraj can convert
between formats, and it will use the file extensions to guess which format
you want, but you can also specify the format on the trajout line.
for example (inside cpptraj):
trajin mdcrd.nc
trajout mdcrd.ascii.x crd
where "crd" here specifies Amber ascii coordinates format. If you use .crd
as the end of the trajectory filename, it will automatically set to crd
format.
for a list of the format keywords and automatic extensions, look at this
page:
https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml#tab:cpptraj-trajformats
there is no need to convert to dcd, pdb or other non-amber formats (unless
that's what you want to do, of course).
On Fri, Dec 3, 2021 at 5:52 AM ankita mehta <mehtaroadies.gmail.com> wrote:
> Hello,
> I am trying to load the trajectory files .mdcrd files in vmd on windows.
> My simulations were run on Amber.
> But everytime i load the files , the following error message is displayed
> on the vmd windows.
> It says " problem reading the crd file".
> I followed following steps:
> 1. select "new molecule "
> 2. Load "parm file " and select file type as "Amber parm 7".
> 3. Then load the trajectory file as "mdcrd" file and select file type as "
> Amber coordinates' '.
> 4. error message displays on the VMD windows "Problem reading CRD file".
>
> P.S. - -I have a windows operating system.
>
> Any help is appreciated !
>
> TIA!
> Ankita
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Received on Fri Dec 03 2021 - 06:30:02 PST
