search

CCPBioSim / fesetup

A tool for setting up free energy simulations.
http://www.ccpbiosim.ac.uk/software
GNU General Public License v2.0
34 stars 18 forks source link

Reindexing of atoms causes problem in mapping #8

Open ppxasjsm opened 5 years ago

ppxasjsm commented 5 years ago

I am not sure if this is intended, but in order to overcome poor mapping one way of doing so is giving an explicit mapping. if I use atom indexes from the input pdb file the explicit mapping will still fail, because FESetup changed the atom indexing in the parametrisation. So only once I have generated a set of vacuum.rst7 and vacuum.parm7 files is it possible to do explicit mapping with the atom indexes in these files.

Input file before parametrisation with atom indexes: input_cats_29

Atom indexes after parametrisation: parametrised_cats_29

skfegan commented 5 years ago

I don't think this is explicitly an FESetup problem. The reindexing is as far as I know happening in one of the dependencies, probably tleap or in a format conversion (from pdb to mol2 or the like).