[AMBER] Conversion NETCDF trajectory to other formats

From: Enrico Martinez via AMBER <amber.ambermd.org>
Date: Fri, 15 Jul 2022 13:33:59 +0200

Dear Amber users!
I am looking for a possibility to convert netcdf trajectory produced
by amber to other formats, particularly to xtc accepted by gromacs.
I've tried to use gmx utilite (that worked fine before!):
gmx trjconv -f ${sim}/prod_*.netcdf -s protein.pdb -o test.xtc
-timestep 10 -pbc no

but it does not work anymore :-)

Program: gmx trjconv, version 2020.1-Ubuntu-2020.1-1

Standard library logic error (bug):
(exception type: St11logic_error)
basic_string::_M_construct null not valid

I have tried to use directly vmd and could open the same file without
problem using
vmd -netcdf my_trajectory.netcdf

is there any way to run vmd in batch without GUI for such conversion?

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Received on Thu Aug 04 2022 - 13:34:22 PDT
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