On Thu, Mar 07, 2013, Shashidhar Rao wrote:
>
> Here is how I obtained the mdcrd file:
>
> 1. ran MD using DESMOND
> 2. input the DESMOND trajectory along with the reference molecule into VMD
> 3. saved the trajectory coordinates in the "crd" file format
>
> Am I mistaken in thinking that the crd file format is the AMBER md
> coordinate file format?
Yes. Trajectory files (in several possible formats) are different beasts than
a restart file. You can use cpptraj to convert one frame of a trajectory file
into a restart file (but it will be missing the box and velocity information).
I'm not sure if Desmond has the ability to output Amber restart files or not.
...dac
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Received on Thu Mar 07 2013 - 12:30:04 PST
