Re: [AMBER] error

From: Wu Xu <>
Date: Sun, 4 Mar 2018 18:25:47 -0600 (CST)

Dear dac,

I used cpptraj to convert binary trajectory to ascii format. perl version of MMPBSA works for ascii format trajectory.



----- Original Message -----
From: "David A Case" <>
To: "AMBER Mailing List" <>
Sent: Saturday, March 3, 2018 4:21:38 PM
Subject: Re: [AMBER] error

On Sat, Mar 03, 2018, Wu Xu wrote:
> Thank you. Do you know the way of converting binary trajectory to ascii
> text format? I searched it and could not find a solution.

You should use cpptraj to do that. The format of your trajin file will
be automatically recognized. If you name the trajout files with a .crd
extension, you should get an ascii trajectory.

The recommended and default trajectory format changed to netcdf (binary)
in Amber16. Unfortunately, I don't think anyone is maintaining the perl
version of MMPBSA anymore [I might be wrong here, and would be glad to
hear that it can read netcdf files....]


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