Dear Yu,
My suggestion for preparing the two endpoints for your NEB simulation is to first create the initial and final topology and coordinate files separately using tleap, and then strip the excess water molecules from the files that include more water using either cpptraj or parmed strip command.
The two masks in the NEB are used for different purposes. tgtfitmask is used to perform RMS fitting in order to minimize the translations and rigid rotations between the neighboring replicas. tgtrmsmask should include all the atoms that are involved in the transition. If you are not sure exactly which atoms to choose, it is better to include all the ones you suspect are playing a role in your transition. Using fewer atoms in each mask will improve the performance, but it is also important to include as many as relevant.
Good luck setting up your NEB simulations.
All the best,
Delaram
-----
Delaram Ghoreishi
Ph.D. Candidate
Department of Physics
University of Florida
________________________________________
From: $B3Ty((B <guoyu1.shanghaitech.edu.cn>
Sent: Sunday, March 3, 2019 10:06 PM
To: amber.ambermd.org
Subject: [AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent?
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 - 23:30:01 PST
