Hi All,
I am preparing the softcore mask for TI simulation. Two copies of the receptor was included in one file with one amino acid mutation for topology file preparation by tleap. It turns out that tleap alters slightly the coordinates of the backbone atoms of the mutated residues which should assumably be identical between the two receptor copies. So now Amber can not identify common backbone atoms because of the coordinate changes. I wonder if there are parameters can be set to adjust the distance tolerance for identification of common atoms in Amber. Or, to disable tleap to change the coordinates?
Best,
Zizhang
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 26 2021 - 11:30:03 PDT
