AMBER Archive (2008)

Subject: Re: AMBER: NAB examples

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 07 2008 - 12:42:34 CDT

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

> 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?

NAB doesn't know anything about the "bintraj" (aka netcdf) option, so that
choice is irrelevant here. Don't confuse "binpos" with "bintraj" (I admit
that might be easy to do!).

If you need to view the results in VMD, use ptraj to convert the trajectory
from binpos to the standard Amber format.

....dac

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