Thank you, your suggestion for outprefix works perfectly.
On 10/30/15 5:45 PM, Jason Swails wrote:
> 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
>>
>>
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--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Fri Oct 30 2015 - 16:30:03 PDT
