Dear Amber users
As I already mentioned, I'm using mdgx to generate parameters for modified
nucleic acids. However, after extraction of the energies calculated by
ORCA, the resulting 'energies_mdgx.dat' file listed the calculated energies
in random(?) order.I'm not quite sure what is happening here since the
extraction should be fairly simple (enclosed file '04_ExtractEnergies').
Using a 'for'-loop with the command sed I generated my own
'energies_sed.dat' file for comparison.
I enclosed the first of the ORCA outputs (Conf1.oout) so you can verify
that this energy does not show up as the first entry in the
'energies_mdgx.dat' file. I also enclosed my own extracted
'energies_sed.dat' file where this is correctly performed.
Additionally, I can add that during the generation of the conformers (also
using mdgx) I lose several conformations so that I don't have 'Conf1.orca'
to 'ConfN.orca' consecutively, resulting in several empty 'ConfX.oout'
files since ORCA is called consecutively in a 'for'-loop. I don't know if
this should bother mdgx during extraction to throw the energies around?
I assume this influences the parameter fitting stage, since the energies
should be attributed respectively to the conformation in the trajectory
file?
Kind regards
Charles-Alexandre Mattelaer
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Received on Mon Jun 12 2017 - 07:00:03 PDT
