Re: [AMBER] Elementary VMD Problem with Amber Trajectory

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 30 Oct 2015 17:45:54 -0400

What prmtop are you using to visualize?

If you strip waters from your trajectory, you can't use a prmtop that still has waters in it to visualize.

You can use the outprefix keyword to strip to print a corresponding prmtop that you CAN use to visualize.

HTH,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
> On Oct 30, 2015, at 5:24 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> 
> 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
> 
> 
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Oct 30 2015 - 15:00:03 PDT