Dear amber users,
I want to do a NEB for a enzyme using explicit solvent and QM/MM. I have start and end structures now, but I do not know how to make sure .prmtop files for two structures are the same.
The only way I can think of is making .prmtop and .inpcrd files for one structure, and change protein's coordinates to second structure in .inpcrd file. Is this reasonable? Or is there any other way?
Also, I'm confused by 'tgtfitmask'. Is it means amber would make sure coordinates for these atoms are the same in all replicates while running NEB? Or these atoms are like "reaction region"? Is it aright if I define my reaction zone with 'tgtfitmask' and atoms actually involved in bond breaking and forming with 'tgtrmsmask'?
thanks for your time. any help would be appreciate!
Yu
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Received on Sun Mar 03 2019 - 19:30:02 PST
