if you just want to visualize and you are using either Linux or OSX, you
can try mdsrv. Work well with AMOEBA topology (I just tried with prmtop and
mdcrd files in $AMBERHOME/test/{amoeba_softcore, amoeba_gb1})
https://github.com/Amber-MD/mdsrv
Hai
On Thu, Aug 18, 2016 at 5:56 PM, Xiaoliu Zhang <xzhan91.lsu.edu> wrote:
> I tried your suggestion...
>
>
> First I loaded pdb file using the file type pdb, and then the VMD OpenGL
> display gave a visualization of my box since the pdb file already includes
> the coordinates.
>
>
> Then, I tried to load inpcrd file for the pdb file using the file type
> amber coordinates ( I also tried to load it under amber restart type ).
> However, it can't cover the coordinate information in the pdb file, and
> there's no change for the graph.
>
>
> I also tried to load the mdcrd file for the pdb file and still no change
> took place. It can't show the trajectory.
>
>
> It seems that I should remove the coordinate information in the pdb file
> first... Do you know how to do this?
>
>
> Thank you!
>
> Xiaoliu
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Received on Thu Aug 18 2016 - 15:30:03 PDT
