AMBER Archive (2009)

Subject: [AMBER] ptraj failure to parse psf input

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Aug 05 2009 - 11:39:57 CDT

Hi,
I'm trying to process output from a NAMD simulation using ptraj (latest
download of AmberTools). While it works fine with some inputs, it fails
with others. Since all of my psf files are generated using VMD and
should follow the same syntax, the only difference I see is that it
fails on larger systems (at least, in my observations). For instance,
27000 atom system is parsed correctly, but 75000+ fails. I'm attaching a
compressed psf file that ptraj is unable to parse. I use 64-bit CentOS
on a Xeon system.
I would greatly appreciate any suggestions.

A side question: I assume that the downloadable AmberTools release is in
fact 1.2, since there is no mention of it anywhere in the content
(docs/changelog refer to 1.0, installation ends with a reference to
1.1). Is this a case of documentation that didn't get updated or
(hopefully, not) the incorrect version packaged for download?

Thanks

Sasha



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