Hi everybody,
I performed pH-REMD in explicit solvent, then I reconstructed the
"trajectory" for each pH using cpptraj. Due to periodic boundary
conditions, my polipeptide is not always centered in the snaphot (i.e. it
looks like it is half outside the solvent box). I would like to know if it
is possible to reorient the vectors and make my polipeptide be in the
center of the solvent box, because I need the coordinates and charges for
further QM calculations.
I hope I have been clear enough!
Thanks,
Elisa
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 01 2016 - 05:30:03 PDT
