Re: [AMBER] pKa Calculation using PMEMD

From: David A Case <>
Date: Thu, 10 Jun 2021 08:06:47 -0400

On Thu, Jun 10, 2021, Monika Pareek wrote:
>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
>TI Mask 1 matches 0 atoms
>TI Mask 2 matches 0 atoms
> 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.

Since you didn't provide any information about your pmemd input, it's hard
to be of much help. Tutorial 7.3 has a lot of information and examples
about the differences between sander and pmemd when it comes to TI.


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Received on Thu Jun 10 2021 - 05:30:03 PDT
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