AMBER Archive (2002)

Subject: RE: Amber Trajectories + VMD (fwd)

From: Nicholson, James D Mr ARO (James.Nicholson_at_apg.amedd.army.mil)
Date: Tue Dec 03 2002 - 17:35:09 CST

Use ptraj to strip out waters then try it. This worked well for me thanks
to a suggestion by Thomas Cheatham. Also, you can have dynamic
hydrogen-bonds during playback in VMD (a nice feature).

-Jim N.

-----Original Message-----
From: amber_at_heimdal.compchem.ucsf.edu
[mailto:amber_at_heimdal.compchem.ucsf.edu]
Sent: Tuesday, December 03, 2002 5:58 PM
To: amber-mail_at_heimdal.compchem.ucsf.edu
Subject: Amber Trajectories + VMD (fwd)

---------- Forwarded message ----------
Date: Tue, 03 Dec 2002 14:44:41 -0600 (CST)
From: joelkp_at_erc.msstate.edu
To: Amber Mailing List <amber_at_heimdal.compchem.ucsf.edu>
Subject: Amber Trajectories + VMD

I'm trying to make an animation in VMD from the trajectory created by an
Amber 7
molecular dynamics run. Here's my input file:

----------
Initial dynamics w/o restraints - AChE / CYX / HID / Solvent / Neutral
 &cntrl
   ntwx = 10,
   ntf = 2, ntb = 2,
   nstlim = 100,
   ntp = 1,
   ntc = 2,
   tempi = 300.0, ntt = 1,
   lastrst = 3000000,
 &end
----------

As you can see, there's only 100 steps, and the coordinates get written out
every 10 steps, indicating that this should be a 10-frame animation. I open
up
VMD 1.7.1, click on 'Molecule', then 'Load From Files', select 'parm and
crd',
and choose my input parameter file and my trajectory file. When I press
'Load
Molecule', VMD proceeds to read in the files, showing a rapidly-increasing
'frames' count. The problem is that this 'frames' count continues to
increase
indefinitely, when it should logically stop at 10. The 'atoms' count also
remains at 0.

Are there any format-conversion steps I should be taking that I'm not? Or is
this not the correct procedure?

-Joel