AMBER Archive (2006)

Subject: Re: AMBER: trouble adding mdcrd files together

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Jun 02 2006 - 18:45:16 CDT

wouldn't the lack of nobox give a larger trajectory (nonsense data
of course) rather than shorter one?
he might have a combination of this and another problem though.

David A. Case wrote:

>On Fri, Jun 02, 2006, Adam Pelzer wrote:
>
>
>>I have run into trouble using ptraj to add two mdcrd files together. My
>>input file was simply this:
>>
>>trajin no_salt_prod.mdcrd
>>trajin no_salt_prod2.mdcrd
>>trajout no_salt_prod1500.mdcrd
>>
>>
>
>Are these periodic or non-periodic trajectories? If they are non-periodic,
>I think you must add the "nobox" keyword for trajout. It's worth a try
>if you do have a non-periodic simulation.
>
>Carlos Simmerling's suggestions were good ones. An additional idea is to
>learn enough about the format of the trajectory files to edit it with a
>text editor, and see what might be wrong.
>
>...good luck...dac
>
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