[gmx-users] Usage of g_spatial

Christopher Neale chris.neale at mail.utoronto.ca
Tue May 7 14:53:07 CEST 2013

Try this:

trjconv -s my.pdb -f my.pdb -o mymod.pdb
g_spatial -s mymod.pdb -f mymod.pdb

For the pre-processing, there must also be AMBER tools that will do this for you if for some reason the above does not work for you (e.g. Option -pbc mol requires a .tpr file for the -s option)


-- original message --

I am analyzing trajectories of an ionic liquid system generated using AMBER
MD package. The force field parameters are typical of this IL system and
not from the existing libraries. Hence, it is difficult for me to generate
a tpr file. I understand that running the g_spatial command needs
pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I
need tpr file for that. So there is  no way of doing g_spatial without a
tpr file is it? Then how do I generate tpr file for my system?

Thanks for all the help

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