29 Aug
2012
29 Aug
'12
3:32 p.m.
I am trying to link the crystal structure of an Fc domain with two Fab structures. I am using the command "minimize spec sel fragment true" on the command line. When various options come up, I've selected "if alternate locations, keep only highest occupancy", "add hydrogens", "add charges", "consider each model in isolation from all others", "also consider H-bonds", and AMBER ff12SB and ANTECHAMBER to assign charges. I've had jobs run overnight that didn't finish. What is a reasonable time for about 8-10 residues to be minimized? Can you suggest any ways to speed this up? Thanks, David