Thank you Justin. Is it possible to choose protein and ligand separately (e.g.
1|13) in the trjconv, since I chose protein-ligand subgroup which was taken as
a whole and ligand can not be distinguished individually ? Or should I do any
modifications in VMD ?
On Monday, March 11, 2019, 6:32:22 PM EDT, Justin Lemkul <jalem...@vt.edu>
wrote:
On 3/11/19 6:01 PM, mary ko wrote:
> Dear all
> How can I make a movie from a protein-ligand simulation in VMD? I opened
> complex.pdb and md-fit.trr and the movie is shown but due to the large
> number of water molecules it freezes after some frames. How can I remove
> solvent molecules from the md-fit.trr? Any other suggestions how to make the
> movie without freezing?
Use trjconv to save whatever subset of coordinates you want.
-Justin
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Justin A. Lemkul, Ph.D.
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