Hello,
I have done the pka calculation using thermodynamic integration as mentioned in the Amber tutorial. The tutorial is based upon using two different topology file corresponding to initial and final state of the system as it is using Sander. I am planning to do through pmemd.cuda to speed up the calculation. I am getting this error while running the simulation:-
TI Mask 1 matches 0 atoms
TI Mask 2 matches 0 atoms
TI region 1: 30912 atoms
TI region 2: 30912 atoms
Checking for mismatched coordinates.
ERROR: timask1/2 must match at least one atom for non-softcore run
Since pmemd reuire only one topology file for both the initial and final state of the system. Could you please help me in performing the same calculation using pmemd.cuda.
Thank you
Thanks and regards,
Monika Pareek
Postdoctoral Researcher
Department of Chemistry-BMC
Uppsala University
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Received on Wed Jun 09 2021 - 23:30:02 PDT
