I am mystified as to what I am doing wrong that I cannot load trajectory
frames into VMD properly. I use PBCs. I have an explicitly solvated
system; I can load the trajectory just fine into VMD. When I strip out
the water,
After some problems, I re-did the calculation to have only 5 frames for
simplicity of analysis.
cpptraj prmtop
trajin 03_Helix.mdcrd 1 5 1
strip :WAT
autoimage
trajout file.crd
go
quit
At no point do I get any errors in cpptraj. When I load the prmtop file
as an Amber7Parm in VMD, followed by loading a Amber Coordinates with
Periodic Box file, no frames actually load in VMD.
I must assume I am missing something obvious?
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Fri Oct 30 2015 - 14:30:03 PDT
