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) Chris. -- 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 -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
