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!
-Hunter
-----Original Message-----
>From: Daniel Roe <daniel.r.roe.gmail.com>
>Sent: Jul 9, 2013 1:31 PM
>To: Hunter Brown <bassoongoon.earthlink.net>, AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Troubles with making a movie in VMD,
>
>Hi,
>
>On Tue, Jul 9, 2013 at 1:23 PM, Hunter Brown <bassoongoon.earthlink.net> 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:
>
>INPUT TRAJECTORIES:
> 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?
>
>-Dan
>
>--
>-------------------------
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>http://home.chpc.utah.edu/~cheatham/
>(801) 587-9652
>(801) 585-9119 (Fax)
>
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Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
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Received on Tue Jul 09 2013 - 13:00:03 PDT
