[gmx-users] Gromacs analysis tools for Namd output
paulclizana at gmail.com
Wed Feb 1 18:35:06 CET 2012
Dear Gromacs users,
I want to use the Gromacs analysis tools for analyzing Namd output files
(*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition
I installed VMD 1.9 and set up
VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is
located the dcdplugin.so )
I verified that VMD_PLUGIN_PATH is pointing out to the right folder.
However when I run for example
g_rmsf_d -f file.dcd -s file.pdb
I got the following error
The file format of file.dcd is not a known trajectory format to GROMACS.
Please make sure that the file is a trajectory!
GROMACS will now assume it to be a trajectory and will try to open it using
the VMD plug-ins.
This will only work in case the VMD plugins are found and it is a
trajectory format supported by VMD.
No plugin for dcd found
Am I doing something wrong? Do I need to do something else?
Any help and advise will be highly appreciate it
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