HI,
Windows version of VMD cannot recognize netcdf format of the trajectories.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Li, Wen <wl2290.cumc.columbia.edu>
Sent: 17 October 2017 21:10
To: amber.ambermd.org; daniel.r.roe.gmail.com
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)
run
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)
run
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.
Thanks!
Wen
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Received on Tue Oct 17 2017 - 09:00:03 PDT
