Re: NAMD 2.6 dcd and breaking XPLOR

From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Wed Feb 13 2008 - 19:50:38 CST

Using wordom (http://www.biochem-caflisch.unizh.ch/wordom/) to read
the DCD headers, I have discovered that NAMD 2.6 headers are
different from 2.5 headers using the same input files. The 2.5 DCDs
invariably have the "Variable PBC" line set to "0", while the 2.6
DCDs have the same line set to "1". Unfortunately, using wordom to
modify the DCD header doesn't solve the problem. I can use wordom to
process the DCD files, so I know they're not completely screwed up.
Does ANYONE have any insight?

On Feb 7, 2008, at 3:15 PM, Neema Salimi wrote:

> Did NAMD 2.6 break dcd files for reading into XPLOR? I use XPLOR
> to do a few things, like extract PDBs from NAMD's binary dcd
> files. I recently switched to 2.6, and now XPLOR complains that
> there's no coordinate sets inside the dcd file. My guess is that
> is has something to how the frames are indexed, but I haven't been
> able to work it out just yet. And yes, my simulations are running
> fine, I can convert binary coordinate restart files and the energy
> outputs look normal. Thanks.
>
> Neema Salimi
> nsalimi_at_msg.ucsf.edu
>
> University of California-San Francisco
> Graduate Group in Biophysics
> Agard Lab
> http://msg.ucsf.edu/agard/
> Lab Phone: (415) 476-5143
>
>
>
>

Neema Salimi
nsalimi_at_msg.ucsf.edu

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143

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