Re: [AMBER] Troubles with making a movie in VMD,

From: Hunter Brown <>
Date: Tue, 9 Jul 2013 13:34:53 -0600 (GMT-06:00)

Oh! Sorry, 2500 is just an arbitrarily large number given to ptraj. The actual number of frames in each trajectory is 1250.

I was able to get the 1,000 frames in VMD by loading a pdb file of my system, and then loading the mdcrd file for that pdb. Before I had tried loading the prmtop as the molecule (which only gave me 189 frames for some reason). Actually, it is odd to me that loading the prmtop as a molecule, and then the trajectory for it did anything at all, because prmtops do not contain any coordinates, no?

It looks like I have the issue sorted out. Sorry for the hasty question, I appreciate the quick response!


-----Original Message-----
>From: Daniel Roe <>
>Sent: Jul 9, 2013 1:31 PM
>To: Hunter Brown <>, AMBER Mailing List <>
>Subject: Re: [AMBER] Troubles with making a movie in VMD,
>On Tue, Jul 9, 2013 at 1:23 PM, Hunter Brown <> wrote:
>> fibril2.mdcrd should have 1,000 frames, however, when I load it in VMD or Chimera, I am only given 189 frames.
>Actually, assuming you indeed have 2500 frames in each trajectory you
>should have 2000 frames total based on your offset (2500/5 = 500, x4).
>What does the 'INPUT TRAJECTORIES:' part of your output read? It
>should be something like:
> 0: [<filename>] is a <format>, Parm <topology name> (<box>) (reading X of N)
> Coordinate processing will occur on M frames.
>In your output, what is each 'X of N', and what is 'M' equal to?
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>(801) 587-9652
>(801) 585-9119 (Fax)
>AMBER mailing list

Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major

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Received on Tue Jul 09 2013 - 13:00:03 PDT
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