Re: [AMBER] trajout format with cpptraj in Ambertools 17

From: Li, Wen <>
Date: Tue, 17 Oct 2017 15:54:53 +0000

Hi Elvis,

I am using linux. Thanks anyway.


From: Elvis Martis <>
Sent: Tuesday, October 17, 2017 6:53:16 AM
To: AMBER Mailing List
Subject: Re: [AMBER] trajout format with cpptraj in Ambertools 17

Windows version of VMD cannot recognize netcdf format of the trajectories.

Best Regards
Elvis Martis
Mumbai, INDIA.

From: Li, Wen <>
Sent: 17 October 2017 21:10
Subject: [AMBER] trajout format with cpptraj in Ambertools 17

Hi Everyone,

My trajectory file was generated with pmemd.cuda, regardless either ntx =7 or 5,

and output file extension is either ncdf or something else, output trajectory is always formatted as NetCDF --- not Amber Coordinates format.

With such trajectory files, I run cpptraj for stripping residues with the input below:

parm del.parm7
trajin eq1.traj (or eq1.ncdf)
strip :1-50
trajout del.traj (or del.ncdf)
output trajectory files del.traj and del.ncdf can't be recognized when viewed with vmd.

I also run rms fit with cpptraj:

parm del.parm7
trajin eq1.traj (or named eq1.ncdf)
rms :1-1000 out rmsd1.agr mass
trajout del.ncdf (or named as del.crd, or del.traj)
the output del.ncdf can't be recognized by vmd again.

All these inputs worked with cpptraj in Ambertools 14 in the past while both input and output files were formatted as crd. Now I am wondering if trajout has to be associated with a specific file extension with cpptraj in Ambertools 17. If so, what is it? Otherwise, what would be the problem.


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Received on Tue Oct 17 2017 - 09:00:04 PDT
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