[AMBER] pKa Calculation using PMEMD

From: Monika Pareek <monika.pareek.kemi.uu.se>
Date: Thu, 10 Jun 2021 06:07:14 +0000


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
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