AMBER Archive (2009)

Subject: Re: [AMBER] ptraj failure to parse psf input

From: Sasha Buzko (
Date: Wed Aug 12 2009 - 16:16:07 CDT

Hi amber developers,
Just checking: has anyone had a chance to look at this ptraj problem?
The unreadable psf file was attached in my first post.. I can post it
again if necessary.

Thanks for your help


Sasha Buzko wrote:
> 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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