AMBER Archive (2008)

Subject: RE: AMBER: NAB examples

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Mon Apr 07 2008 - 11:43:06 CDT

Thanks Dave. Is there any problem in my file? What is the difference the
option nobintraj can make? Can the trajectory be viewed by VMD?

Thanks,
Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Monday, April 07, 2008 11:27 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: NAB examples

On Mon, Apr 07, 2008, Hu, Shaowen (JSC-SK)[USRA] wrote:

> I compiled with nobintraj option. But the file I obtained is not
> readable as AMBER.

NAB writes trajectories in "binpos" format. This is really kind of
obsolete, and should be changed. But for now, you should be able to use
ptraj to read in and analyze these trajectories, or to convert them to
some other format.

...good luck...dac

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